Re: [Freesurfer] Flipped left to right hemisphere subjects

[Greve, Douglas N.,Ph.D.]

Is the  volume actually left-right reversed?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lutz,Olivia (BIDMC - 
Psychiatry) 
Sent: Monday, August 20, 2018 4:55:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Flipped left to right hemisphere subjects


Hi Doug and Bruce,


thank you for the quick reply. As a follow-up question, we've edited our 
brainmasks for a dataset and want to flip some subjects left to right. I found 
instructions to flip the scans, however they are for the nu.mgz file 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal). Is is possible 
to apply this

mri_convert --in_orientation​ command to change the left and right labels of 
the brainmask so we don't have to re-edit as opposed to applying it to the 
nu.mgz file and regenerating the brainmask?

Thanks!
Olivia




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Re: [Freesurfer] Interpretation of pcc.mgh for negative contrasts

[Greve, Douglas N.,Ph.D.]

gamma and pcc should be the same sign. The relationship to the sign of 
beta depends on your contrast. If beta is negative and your contrast 
element is negative, then you will get a positive gamma and pcc.

On 09/13/2018 02:15 PM, Nicola Toschi wrote:
> External Email - Use Caution
> Thank you Doug,
>
> that was exactly the question...
>
> it may be a trivial one but I have been messing aroung with several 
> effects size calculation for a while and just wanted to make sure. So 
> negative contrast (-1), negative beta.mgh, positive (?) gamma.mgh, and 
> negative pcc.mgh withing the same significant cluster?
>
> Thanks!!!
>
> nicola
>
>
>
> On 09/13/2018 07:39 PM, Douglas N. Greve wrote:
>> not sure what your question is. The pcc should have the same sign as the
>> contrast.
>>
>> On 09/13/2018 12:20 PM, Nicola Toschi wrote:
>>>   External Email - Use Caution
>>>
>>> Hi List,
>>>
>>> a dimple question about using partial correlation (pcc.mgh) as effect
>>> size measure. I am running multivariate regression and setting positive
>>> and negative contrasts one variable at a time, e.g. a design matrix 
>>> with
>>> columns like
>>>
>>> Intercept Age Gender Fact1 Fact2 
>>>
>>> and a bunch of contrasts like
>>>
>>> 0   0  0    1    0
>>>
>>> 0   0  0    -1 0
>>>
>>> Now let's say the second contrast gives me a significant results after
>>> MC correction in a certain cluster, what sign should i expect in PCC in
>>> that cluster (on average)?
>>>
>>> Thank you very much in advance,
>>>
>>> Nicola
>>>
>>>
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Re: [Freesurfer] Questions on multiple inputs

[Greve, Douglas N.,Ph.D.]

Most of FS/recon-all will run using the T1 only. The T2 can be used to refine 
the pial surface (-T2  T2file.mgz -T2pial)


On 9/18/18 4:56 AM, limiyu wrote:

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Dear developers

I have a question on how could I segment two registered MRI images and 
get only one segmentation result, by command recon-all ?

In details, I have two MRI images which are T1-weighted and 
T2-weighted. They are the photos of one brain. How could I input both of them 
into Freesufer and output one segmentation result, which takes both of the 
input into consideration.
I know that command "recon-all -all" could output the segmentation but 
do not know what to do when there are multiple inputs.

Looking forward to your reply
Thank you
Mingyuan Liu








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Re: [Freesurfer] if: missing file name

[Greve, Douglas N.,Ph.D.]

Not sure what is going on there. Is that really the only thing that gets 
printed out? Run recon-all with -debug as the first option. Capture and 
send us the terminal output (ie, the stuff that gets printed to the 
screen). Also, please make sure to include previous correspondence in 
your email so we know what the context is.
doug


On 09/19/2018 11:35 AM, Yacila Isabela Deza Araujo wrote:
>  External Email - Use Caution
>
> Dear Freesurfer experts,
>
> Please find in the attachment a file with the errors I get when I try to 
> follow the examples of recon-all
>
> Thanks a lot for your support,
>
> Yacila
>
>
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Re: [Freesurfer] if: missing file name

[Greve, Douglas N.,Ph.D.]

It looks like you do not have the SUBJECTS_DIR env variable set.

On 09/19/2018 01:31 PM, Yacila Isabela Deza Araujo wrote:
>  External Email - Use Caution
>
> Hello,
>
> Please, find in the attachment the capture of the terminal output. It is 
> basically the same that I get when I run it from the freesurfer/subjects 
> directory.
>
> I also need to say that the problem is only with this Mac. It runs without 
> any problem in a Linux computer.
>
> Thanks a lot for your support
>
> Yacila
>
>> --
>>
>> Message: 1
>> Date: Wed, 19 Sep 2018 15:35:08 +
>> From: Yacila Isabela Deza Araujo
>>  
>> Subject: [Freesurfer] if: missing file name
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Message-ID: 
>> Content-Type: text/plain; charset="us-ascii"
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer experts,
>>
>> Please find in the attachment a file with the errors I get when I try to 
>> follow the examples of recon-all
>>
>> Thanks a lot for your support,
>>
>> Yacila
>> -- next part --
>> A non-text attachment was scrubbed...
>> Name: Freesurfer error.rtf
>> Type: text/rtf
>> Size: 1457 bytes
>> Desc: Freesurfer error.rtf
>> Url : 
>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180919/ae9daaec/attachment-0001.rtf
>> -- next part --
>> An embedded and charset-unspecified text was scrubbed...
>> Name: ATT1.txt
>> Url: 
>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180919/ae9daaec/attachment-0001.txt
>>
>> --
>>
>> Message: 2
>> Date: Wed, 19 Sep 2018 15:50:56 +
>> From: "Greve, Douglas N.,Ph.D." 
>> Subject: Re: [Freesurfer] if: missing file name
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Message-ID: <7cb10386-9603-c3bf-0202-fbe729baa...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="Windows-1252"
>>
>> Not sure what is going on there. Is that really the only thing that gets
>> printed out? Run recon-all with -debug as the first option. Capture and
>> send us the terminal output (ie, the stuff that gets printed to the
>> screen). Also, please make sure to include previous correspondence in
>> your email so we know what the context is.
>> doug
>>
>>
>> On 09/19/2018 11:35 AM, Yacila Isabela Deza Araujo wrote:
>>>  External Email - Use Caution
>>>
>>> Dear Freesurfer experts,
>>>
>>> Please find in the attachment a file with the errors I get when I try to 
>>> follow the examples of recon-all
>>>
>>> Thanks a lot for your support,
>>>
>>> Yacila
>>>
>>>
>>> ___
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>>
>>
>>
>> --
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>> End of Freesurfer Digest, Vol 175, Issue 25
>> ***
>>
>>
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Re: [Freesurfer] Using freesurfer without intensity normalization

[Greve, Douglas N.,Ph.D.]

You'll still need to have WM at about 110 or else FS will fail.

On 09/19/2018 02:48 PM, Raquib Ridwan wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I would like to know if intensity normalization(not bias field 
> correction) so that white-matter is ~110 and gm is ~60 is necessary 
> for freesurfer segmentation. Will intensity normalization using other 
> methods still work for freesurfer segmentation?
>
>
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Re: [Freesurfer] Urgent help with preprocessing pipeline

[Greve, Douglas N.,Ph.D.]

It is hard to say. While a p-value changing from .02 to .2 seems like a 
lot, it does not really take much change in the values. I would look at 
the CVs for the individual subjects both in cross and long and see which 
ones are causing the change. My experience is that long is much better 
than cross for longitudinal data.

On 09/19/2018 01:18 PM, Martin Juneja wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> version of FreeSurfer.
>
> I used cross-sectional pipeline to identify ROIs (from Desikan atlas) 
> with significant difference in cortical volume (CV) between controls 
> and *patients (subjects 1-40, baseline)*, say I get ROIs: R1, R2 and R3.
>
> I am using these ROIs (R1, R2 and R3) for further analysis to 
> determine the effect of two treatments: *T1 (placebo) (for subjects 1 
> to 20) and T2 (active) (for subjects 21 to 40)*, compared to their 
> corresponding baseline.
>
> I compared CV of these ROIs (R1, R2 and R3): *T1 vs. baseline and T2 
> vs. baseline* using both cross-sectional as well as longitudinal pipeline.
>
> *Using cross-sectional pipeline:* I found there is significant 
> improvement in CV (p = 0.019) for these ROIs for treatment T2 compared 
> to baseline and no change for placebo treatment T1.
> *Using longitudinal pipeline: *There is little improvement in CV (p = 
> 0.2) for these ROIsfor treatment T2 compared to baseline and no change 
> for placebo treatment T1.
>
> I was wondering why I am getting results so different between these 
> pipelines, and which pipeline suits better in such comparison when my 
> ROIs are identified using cross-sectional pipeline, but further 
> analysis of these ROIs involved longitudinal comparison.
>
> I would really appreciate any help (as early as possible).
>
> Thank you so much !
>
>
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Re: [Freesurfer] linux data and macbook

[Greve, Douglas N.,Ph.D.]

what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for 
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook 
>
>
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Re: [Freesurfer] Ynt: linux data and macbook

[Greve, Douglas N.,Ph.D.]

sorry, we need way more detail

On 9/20/18 11:59 PM, emre wrote:

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thalamus and hippocampus

Gönderen Outlook<http://aka.ms/weboutlook>

Gönderen: Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu> adına 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
Gönderildi: 21 Eylül 2018 Cuma 00:15
Kime: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Konu: Re: [Freesurfer] linux data and macbook

what segmentation?

On 09/20/2018 12:53 PM, emre wrote:
>
> External Email - Use Caution
>
>
> hi freesurfer team,
>
> I analyzed the data at linux, this data i can use in macbook for
> segmantation?
> (linux only reconall -all, other analyze in macbook)
>
> Is it possible without problems?
>
>
> thanks, good luck
>
> Gönderen Outlook <http://aka.ms/weboutlook>
>
>
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Re: [Freesurfer] mri_glmfit-sim error

[Greve, Douglas N.,Ph.D.]

Can you verify that the followign file exists, that you have read permission, 
and that you can successfully load it into freeview? 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white

On 9/21/18 11:41 AM, C.P.E. Rollins wrote:
   External Email - Use Caution
Hello Freesurfer Developpers,

I'm trying to use mri_glmfit-sim to make clusterwise corrections but am running 
into the following error:
- XFM matrix (RAS2RAS) ---
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;
MRISread('\ufffd\ufffd): could not open file
No such file or directory

Reading source surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
mri_surfcluster.bin: could not read surface 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
No such file or directory

I've attached here the log file. I was wondering if you had any insights into 
the error?

Thanks a lot for your help.

Colleen



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Re: [Freesurfer] GLM

[Greve, Douglas N.,Ph.D.]

you need to have four classes, young-female, young-male, old-female, old-male

On 9/21/18 3:15 AM, 郑凤莲 wrote:

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Dear experts,

I am using FS 6.0 for some studies. I want to calculate the thickness 
difference between males and females in two group, Young group and Old group. 
In DODS model:

The first step: creat a FSDG file:
GroupDescriptorFile 2
Title Tutorial
Class Young, Female
Class Old, Male
Variables education
Input P01 Young Female 11
Input P02 Old  Male 9
Input P03 Young Male 10

The second step: creat contrast matrix
1 -1 -1 1 0 0 0 0
Is it right? I am not sure if the FSDG file and contrast file are right. 
Waiting for you to solve my problem.
Thanks for your attention and help.

Sincerely,
Zheng







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Re: [Freesurfer] make_average_subject error

[Greve, Douglas N.,Ph.D.]

Can you send the make_average-subject command and log file?

On 9/21/18 7:03 AM, C.P.E. Rollins wrote:
   External Email - Use Caution
Hello Freesurfer Developpers,

I'm attempting to make a study specific template using all of my subjects as 
input using the make_average_subject command, but am receiving the following 
error:
Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault (core dumped)
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 
GNU/Linux

recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 2018

I've attached here the full log file.

I read in this forum: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html to 
try installing the following patch: 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
and had asked our computing support team to install it before the current run 
of make_average_subject, so the error seems to be happening despite the patch. 
I would greatly appreciate your suggestions for resolving the error.

Thanks very much,

Colleen



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Re: [Freesurfer] calculated cortical thickness from segmented binary gray matter and white matter images from other software

[Greve, Douglas N.,Ph.D.]

Not by default with our software. You could create white and pial surfaces, but 
they would not be very accurate, and there would be no way to fit the surfaces 
to the segmentations.

On 9/21/18 10:21 AM, 
yuanchao.zha...@gmail.com wrote:

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Dear experts,

Is there any way I can calculate the cortical thickness based on gray matter 
and white matter binary images from other software.
I mean I have a image in native space with white matter voxels labelled as 10 
and gray matter voxels labelled as 5.
Is there any way I can manage to calculate the cortical maps from this image 
using freesurfer?

Thanks a lot!

Best,

Yuanchao Zhang


yuanchao.zha...@gmail.com



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Re: [Freesurfer] Missing files in mri_glm

[Greve, Douglas N.,Ph.D.]

What version of FS are you using? The pcc may only be in the v6.

On 09/24/2018 12:10 PM, srishti goel wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am running analysis to compare group difference in thickness between 
> two groups. I followed all the steps outlined on the wiki: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis.
> Everything seemed to work fine except I didn't get the following files 
> in each contrast's directory
>
> efficiency.dat
> pcc.mgh
> z.mgh
>
> I don't understand why those files don't show up as I didn't get any 
> errors. Any help is appreciated.
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu 
> skype: srishti.goel12
>
>
>
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Re: [Freesurfer] Missing files in mri_glm

[Greve, Douglas N.,Ph.D.]

I can't remember that far back:), but it would not surprise me if they 
were not there in 5.3. You can always use the v6 mri_glmfit with 5.3 data.

On 09/24/2018 12:39 PM, srishti goel wrote:
>
> External Email - Use Caution
>
> Alright, yes I am using 5.3. What about the efficiency and z files?
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu <mailto:srish...@email.unc.edu>
> skype: srishti.goel12
>
>
>
> On Mon, Sep 24, 2018 at 12:36 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> What version of FS are you using? The pcc may only be in the v6.
>
> On 09/24/2018 12:10 PM, srishti goel wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > I am running analysis to compare group difference in thickness
> between
> > two groups. I followed all the steps outlined on the wiki:
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis.
> > Everything seemed to work fine except I didn't get the following
> files
> > in each contrast's directory
> >
> > efficiency.dat
> > pcc.mgh
> > z.mgh
> >
> > I don't understand why those files don't show up as I didn't get
> any
> > errors. Any help is appreciated.
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> <mailto:srish...@email.unc.edu> <mailto:srish...@email.unc.edu
> <mailto:srish...@email.unc.edu>>
> > skype: srishti.goel12
> >
> >
> >
> > ___
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Re: [Freesurfer] ERROR: dimension mismatch between X and contrast

[Greve, Douglas N.,Ph.D.]

You have 3 groups and 2 covariates, so you will have 3*(2+1)=9 
regressors, in this order
ADHD-offset COM-offset TD-offset ADHD-Age COM-Age TD-AGE ADHC-IQ COM-IQ 
TD-IQ
You will need to have a single value for each regressor in your contrast 
matrix, meaning that you should have 9 values. You have 10 values, thus 
the error.



On 09/27/2018 09:39 AM, Backhausen, Lea wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I get this error message when running group analysis on cortical 
> thickness using glmfit:
> ERROR: dimension mismatch between X and contrast 
> Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols
>
> Please find attached the FSGD file, the contrast file and the terminal 
> output below.
>
> I want to do ANCOVA with three groups (ADHD, COM and TD) controlling 
> for the effects of age and IQ.
> So I assume the regressors would be ADHD COM TD age IQ and my contras 
> matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two 
> tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and 
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V.
>
> Can anybody help me out? Where am I wrong? Why does glmfit assume X 
> has 9 cols?
>
> Any help would be much appreciated, thank you in advance!
>
> Best
> Lea
>
>
> Terminal Output:
> mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd 
> FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx 
> --surf fsaverage rh --cortex --glmdir 
> rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
> gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 13.6015 1.73148
> 1 IQ 107.288 11.1649
> Class Means of each Continuous Variable
> 1 ADHD  13.7193 104.3478
> 2 COM  12.8657 105.3929
> 3 TD  14.0119 112.3784
> INFO: gd2mtx_method is dods
> Reading source surface 
> /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/surf/rh.white
> Number of vertices 163842
> Number of faces    327680
> Total area 65020.839844
> AvgVtxArea   0.396851
> AvgVtxDist   0.717994
> StdVtxDist   0.193566
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> cwd 
> /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS
> cmdline mri_glmfit.bin --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd 
> FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx 
> --surf fsaverage rh --cortex --glmdir 
> rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
> sysname  Darwin
> hostname edr06188.dip.tu-dresden.de
> machine  x86_64
> user Lea
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y 
> /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh
> logyflag 0
> usedti  0
> FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd
> labelmask 
> /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
> Loading y from 
> /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh
>    ... done reading.
> INFO: gd2mtx_method is dods
> Saving design matrix to 
> rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat
> Computing normalized matrix
> Normalized matrix condition is 1027
> Matrix condition is 4.07619e+06
> Found 149926 points in label.
> Pruning voxels by thr: 1.175494e-38
> Found 149926 voxels in mask
> Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh
> Reshaping mriglm->mask...
> search space = 74490.844410
> ERROR: dimension mismatch between X and contrast 
> Contrasts/ADHD_COM_TD_age_IQ.mtx   X has 9 cols, C has 10 cols
>
>
>
>
>
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Re: [Freesurfer] tksurfer-sess frame time course question

[Greve, Douglas N.,Ph.D.]

answwers below

On 09/27/2018 05:44 AM, 伊藤匠吾 wrote:
>
>
> Hello,
>
> I am new to FreeSurfer.
>
> I conducted an experiment with event-related design.
> There were eight non-fixation conditions. In every trial, a simple 
> stimulus was presented for about 1.5 sec, and the subject made a 
> button press.
>
> I did the following analyses:
>
> preproc-sess -df sessdirfile -s YY03 -per-run -fwhm 5 -sliceorder 
> siemens -surface fsaverage lhrh -mni305  -fsd bold
>
> mkanalysis-sess -a YY.sm5.lh -surface fsaverage lh -TR 2 -p OWN.par 
> -event-related -fsd bold -per-run -fwhm 5 -nconditions 8 -mcextreg  
> -fir 4 24  -polyfit 2 -force
>
> mkcontrast-sess -analysis YY.sm5.lh -contrast all_null -a 1 -a 2 -a 3 
> -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -rmprestim
>
> selxavg3-sess -df sessdirfile -sf sessid -analysis YY.sm5.lh
>
> then, I checked the data with tksurfer-sess (tksurfer-sess -df 
> sessdirfile -s YY03 -analysis YY.sm5.lh -contrast all_null).
> When clicked Overlay/Configure, I see Frame (0-8). Frame #1 shows 
> clear task-related activations (visual, auditory, motor areas).
> Because I used -fir 4 24, I think I should have 12 time points, not 9.
> I am currently using version 6, but I also checked the data with 
> version 5, confirmed the same outcome.
> raw plots by tksurfer-sess (version 5) showed hemodynamic responses 
> for -4 sec to 20 sec. So the data seem to have correct length.
>
> Then, I created several contrasts with -setwdelay for all_null 
> weigting different time points like this
> w1_all_null : 1 0 0 0 0 0 0 0 0 0 0 0
> w3_all_null : 0 0 1 0 0 0 0 0 0 0 0 0
> w5_all_null : 0 0 0 0 1 0 0 0 0 0 0 0
> w7_all_null : 0 0 0 0 0 0 1 0 0 0 0 0
>
> with the following command, I see 4 frames, which probably correspond 
> to each contrast.
> tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast 
> w1_all_null -contrast w3_all_null -contrast w5_all_null -contrast 
> w7_all_null
>
> However, when changing "frame" gives exactly the same image.
>
> (1) why did I get Frame (0-8) for my data that should have 12 frames?
When you use -rmprestim, it subtracts the mean of the prestim baseline 
AND removes the prestim time points (-4 -2 and 0) so you only end up 
with 9 frames.
> (2) how can I visualize contrasts created with -setwdelay?
Your visualization command is correct. I don't understand why you are 
seeing the same image for each frame. Can you load them separately and 
see if they are different?
> I would appreciate for any comments/suggestions.
>
> Here is my environment:
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME       /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /Users/guest/Documents/FreeSurfer/subjects
> MNI_DIR           /Applications/freesurfer/mni
> FSL_DIR           /usr/local/fsl
> --
>
> Thank you!
> Shoo
>
>
>
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Re: [Freesurfer] Reporting Cohen's D for a significant cluster

[Greve, Douglas N.,Ph.D.]

This is the behavior in 6.0. It has been fixed in the deev version. I 
think it is possible to download just the dev version of freeview. 
Otherwise, you could do your computation in matlab with
c = MRIread('cohensd.mgh');
c.vol(vertexno+1)


On 09/26/2018 02:34 PM, Maksimovskiy, Arkadiy wrote:
>
> Hi Bruce,
>
> I am including the previous correspondence below, but here is a quick 
> summary:
>
> My goal is to get the Cohen’s D value for a max vertex of a 
> significant cluster.
>
> I entered the max vertex number in the bottom left of the freeview 
> window (cursor window), where it says vertex. When I hit enter, RAS 
> coordinates change, but the vertex # goes back to what it was 
> previously and Cohen’s D (loaded as an overlay) does not change. The 
> cohen’s D only changes when I move the mouse and click manually.
>
> I am attaching two screenshots of the before, during entry, and after 
> to illustrate the process.
>
>   * arkadiy
>
> Previous Correspondence:
>
> Hi Arkadiy
>
> can you include the previous correspondance so we have context? And 
> what window did you enter numbers? Was it the left hand side of the 
> info window (under "cursor")?
>
> cheers
>
> Bruce
>
> On Wed, 26 Sep 2018, Maksimovskiy, Arkadiy wrote:
>
> Hi Bruce,
>
> I wanted to follow up on this as I was unsuccessful in doing what you 
> suggested
>
> using Freeview
>
> (2.0)- entering numbers into the window does not change anything. 
> Might there
>
> be another way to find
>
> out the Cohen’s D?
>
> Thank you for your help,
>
> Arkadiy
>
> -- 
>
> Arkadiy L. Maksimovskiy, Ph.D.
>
> Postdoctoral Research Fellow
>
> McLean Imaging Center, McLean Hospital
>
> Department of Psychiatry, Harvard Medical School
>
>
>   Re: [Freesurfer] Reporting Cohen's D for a significant cluster
>   
> 
>
> 2018-09-20 
> Thread
>  
> 
>  
> Maksimovskiy, Arkadiy 
> 
>
> Hi Bruce,
> Thank you so much for the tip and the quick response.
> For some reason, the position and Cohen’s D value do not change when I 
> input
> the vertex and I think this might be due to an outdated Freeview 
> version (2.0)
> that I am using.
> I attempted to load the new one from this link:
> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
> But I am getting an error: The requested URL
> /pub/dist/freesurfer/freeview/freeview_osx.tar.gz was not found on 
> this server.
> I was wondering if you have this file available at another location?
> Thanks again,
> arkadiy
> --
> Arkadiy L. Maksimovskiy, Ph.D.
> Postdoctoral Research Fellow
> McLean Imaging Center, McLean Hospital
> Department of Psychiatry, Harvard Medical School
> --
> Arkadiy L. Maksimovskiy, Ph.D.
> Postdoctoral Research Fellow
> McLean Imaging Center, McLean Hospital
> Department of Psychiatry, Harvard Medical School
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>
>
>
>   Re: [Freesurfer] Reporting Cohen's D for a significant cluster
>   
> 
>
> 2018-09-20 
> Thread
>  
> 
>  
> Bruce Fischl 
> 
>
> Hi Arkadiy
> if you have the surface loaded you can always type a vertex number into
> the info field (that shows the current selected vertex) at the bottom of
> the freeview window. It will then jump to that vertex, and adjust the 
> views
> accordingly
> cheers
> Bruce
> On Thu, 20 Sep 2018, Maksimovskiy, Arkadiy wrote:
> Update: It occurred to me that reporting it for the max verted might 
> be the
> best idea. In this case,
> might anyone know what is the best way to navigate the Freeview to a 
> specific
> vertex number (is
> there a place where I can inpu

Re: [Freesurfer] Clarification about .annot file format

[Greve, Douglas N.,Ph.D.]

Thanks Chris, can you point us to the offending wiki page?
doug

On 9/28/18 12:44 PM, Christopher Markiewicz wrote:

External Email - Use Caution

Hi all,


I believe I've gotten to the bottom of this, and the problem is incorrect 
documentation, both in the read/write_annotation.m files and in the wiki.


Taking the FreeSurfer C source as the de facto specification, we can refer to 
the colortab.c file. Here, the labels are not constructed or decoded using the 
transparency (255 - alpha) information at all, but are simply (R + G << 8 + B 
<< 16).


For more complete discussion, see:


https://github.com/nipy/nibabel/issues/649#issuecomment-424755969


I think the most parsimonious resolution of this confusion is simply to update 
the documentation on the wiki page (I cannot; someone with permissions will 
need to), and to patch the MATLAB code to build its labels from RGB values 
alone. I will submit a patch to the GitHub branch.

Please let me know if I've gotten something wrong.

Best,
Chris Markiewicz


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of paul mccarthy 

Sent: Thursday, September 20, 2018 11:39:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Clarification about .annot file format


External Email - Use Caution

Howdy,

There is a discussion regarding the .annot file format over at the nibabel 
github repository, regarding the interpretation of the flag/alpha value:

https://github.com/nipy/nibabel/issues/649

If one wishes to create an .annot file with colours that have a transparency 
value, how should it be stored in the file? By piecing together the information 
from the freesurfer code [1,2], and Graham Wideman's helpful notes [3], I came 
to the conclusion that alpha values should be stored as 1-the actual value. But 
it would be great to get some clarification on this from somebody who knows 
more than me

Thanks very much,

Paul McCarthy

[1] https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m
[2] https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m
[3] 
https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation



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Re: [Freesurfer] Clarification about .annot file format

[Greve, Douglas N.,Ph.D.]

Is this the offending line? or is there more?
value = (A * 2563) + (B * 2562) + (G * 256) + (R)


On 9/28/18 1:03 PM, Christopher Markiewicz wrote:

External Email - Use Caution

Hi Doug,


The relevant wiki page is: 
https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation


Chris


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Friday, September 28, 2018 12:47:36 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Clarification about .annot file format

Thanks Chris, can you point us to the offending wiki page?
doug

On 9/28/18 12:44 PM, Christopher Markiewicz wrote:

External Email - Use Caution

Hi all,


I believe I've gotten to the bottom of this, and the problem is incorrect 
documentation, both in the read/write_annotation.m files and in the wiki.


Taking the FreeSurfer C source as the de facto specification, we can refer to 
the colortab.c file. Here, the labels are not constructed or decoded using the 
transparency (255 - alpha) information at all, but are simply (R + G << 8 + B 
<< 16).


For more complete discussion, see:


https://github.com/nipy/nibabel/issues/649#issuecomment-424755969


I think the most parsimonious resolution of this confusion is simply to update 
the documentation on the wiki page (I cannot; someone with permissions will 
need to), and to patch the MATLAB code to build its labels from RGB values 
alone. I will submit a patch to the GitHub branch.

Please let me know if I've gotten something wrong.

Best,
Chris Markiewicz


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of paul mccarthy 
<mailto:pauldmccar...@gmail.com>
Sent: Thursday, September 20, 2018 11:39:53 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Clarification about .annot file format


External Email - Use Caution

Howdy,

There is a discussion regarding the .annot file format over at the nibabel 
github repository, regarding the interpretation of the flag/alpha value:

https://github.com/nipy/nibabel/issues/649

If one wishes to create an .annot file with colours that have a transparency 
value, how should it be stored in the file? By piecing together the information 
from the freesurfer code [1,2], and Graham Wideman's helpful notes [3], I came 
to the conclusion that alpha values should be stored as 1-the actual value. But 
it would be great to get some clarification on this from somebody who knows 
more than me

Thanks very much,

Paul McCarthy

[1] https://github.com/freesurfer/freesurfer/blob/dev/matlab/read_annotation.m
[2] https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m
[3] 
https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles#Annotation



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Re: [Freesurfer] error glm-fit-sim

[Greve, Douglas N.,Ph.D.]

What says that? What command are you running? What is the other terminal 
output?

On 10/01/2018 04:54 AM, Caroline Beelen wrote:
>
> External Email - Use Caution
>
> Dear FS,
>
> I followed the group analysis page for glm analysis and it worked fine 
> until the final step. I’m using version 5.3. After performing 
> glm-fit-sim it says “glm-fit done” (for all files), but when trying to 
> open these it says:
>
> “Reading colortable from annotation file…
>
> Colortable with 1 entries read (originally none)
>
> Colortable with 1 entries read (originally none)
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> Resource temporarily unavailable”
>
> (etc..)
>
> It opens, but nothing is visible and I have the feeling it cannot open 
> color files??
>
> MRI glmfit gives positive clusters for some values. I therefore used 
> the abs sign for glm-fit-sim.
>
> What might be wrong?
>
> Thanks. Caroline
>
>
>
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Re: [Freesurfer] Convert sig.cluster.mgh file to a binary mask in .nii format

[Greve, Douglas N.,Ph.D.]

assuming this is a surface-based analysis, then you'll need to run mri_surf2vol 
to convert it into a volume using fsaverage as the subject. Run it with --help 
to get more info

On 10/2/18 5:14 AM, Carme Uribe Codesal wrote:

External Email - Use Caution

Dear FreeSurfer users,

I am trying to extract a binary mask from the file 
cache.th13.abs.sig.cluster.mgh (I want a ROI from the clusters p<0.05) and 
convert this mask into a .nii file.

I have found a previous message in the forum that reccomends using mri_binarize:

mri_binarize --i cache.th13.abs.sig.cluster.mgh --min 1.3 --o lh_AP.mgh

And from this output I have run:

mri_convert --in_type mgh --out_type nii --out_orientation RAS lh_AP.mgh 
lh_AP.nii


However, I can't visualize the lh_AP.mgh and of course the lh_AP.nii is not 
created properly when I try to visualize it with mricron.

Another command that I have tried without success is:

mri_surf2surf --sval lh_AP.mgh --tval test.nii --hemi lh


How can I get the mask to operate with it in FSL for example?

Thanks in advance!

Carme Uribe



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Re: [Freesurfer] analyzing and reporting parcellation results

[Greve, Douglas N.,Ph.D.]

Unless you have an a priori hypothesis about an effect in a particular ROI, 
then you need to correct for multiple ROIs

On 10/2/18 7:25 AM, Tamir Eisenstein wrote:

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Hi FS experts,
When I'm analyzing regional volumes/thickness using one of the atlases ROI's 
parcellation, and for example want to compare all the ROI's between two groups, 
should I correct for multiple comparisons (for the entire number of the atlas 
ROI's)? or is it acceptable to report the results as it is?

Best,
Tamir



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Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

[Greve, Douglas N.,Ph.D.]

What shell are you using? Try using cshell or tcshell to see if it works.

On 10/2/18 4:56 AM, k3...@free.fr wrote:
>  External Email - Use Caution
>
> Hi FS team,
>
> I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything 
> runs well for most of the subjects that I process so first thanks for this 
> great tool.
> I am facing an issue with a JPEG compressed DICOM series that I am not able 
> to precess, I always get the following error during "mri_convert" procedure 
> (before calling recon-all), I also wrote the last command that produces this 
> error:
>
> fsdcmdecompress --i freesurfer_18/6858304 --o 
> /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& 
> /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out
> sh: 1: Syntax error: Bad fd number
>
> After some investigations, it looks it is related to the way standard outputs 
> are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file 
> (which is missing by the way).
> It looks like ">&" redirection is not a correct syntax in bash (the shell I 
> am using), so I tried with others but unfortunately none of them worked so 
> far (zsh, tcsh, csh, sh).
>
> Do you have any recommendation for the way to use "mri_convert" tool? or any 
> other tool that could convert DICOM to nifty efficiently?
>
> Thanks for your feedbacks.
>
> Regards,
> Florent
>
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Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

[Greve, Douglas N.,Ph.D.]

Sorry, I meant to change your default shell. That command is being run 
using the system() command from inside of a c-program, which undoubtedly 
starts your default shell. Just see if it works.

On 10/02/2018 10:36 AM, k3...@free.fr wrote:
>  External Email - Use Caution
>
> I am using bash shell but I tried with many others as mentioned in my first 
> post (zsh, tcsh, csh, sh) and nothing worked so far...
>
>
> - Mail original -
> De: "Douglas N. Greve,Ph.D." 
> À: freesurfer@nmr.mgh.harvard.edu
> Envoyé: Mardi 2 Octobre 2018 15:18:14
> Objet: Re: [Freesurfer] Error during decompression of DICOM JPEG compressed 
> series
>
> What shell are you using? Try using cshell or tcshell to see if it works.
>
> On 10/2/18 4:56 AM, k3...@free.fr wrote:
>>   External Email - Use Caution
>>
>> Hi FS team,
>>
>> I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and 
>> everything runs well for most of the subjects that I process so first thanks 
>> for this great tool.
>> I am facing an issue with a JPEG compressed DICOM series that I am not able 
>> to precess, I always get the following error during "mri_convert" procedure 
>> (before calling recon-all), I also wrote the last command that produces this 
>> error:
>>
>> fsdcmdecompress --i freesurfer_18/6858304 --o 
>> /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& 
>> /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out
>> sh: 1: Syntax error: Bad fd number
>>
>> After some investigations, it looks it is related to the way standard 
>> outputs are redirected to 
>> "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing 
>> by the way).
>> It looks like ">&" redirection is not a correct syntax in bash (the shell I 
>> am using), so I tried with others but unfortunately none of them worked so 
>> far (zsh, tcsh, csh, sh).
>>
>> Do you have any recommendation for the way to use "mri_convert" tool? or any 
>> other tool that could convert DICOM to nifty efficiently?
>>
>> Thanks for your feedbacks.
>>
>> Regards,
>> Florent
>>
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Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

[Greve, Douglas N.,Ph.D.]

The command is being run from inside of a C-file using the system 
command, so there is no way for them to change it

On 10/02/2018 01:43 PM, Dicamillo, Robert wrote:
> It may be complaining about >& for redirection.  Try using 2>&1 instead.
>
>> On Oct 2, 2018, at 4:56 AM, k3...@free.fr  wrote:
>>
>> sh: 1: Syntax error: Bad fd number
>
>
>
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Re: [Freesurfer] output values of vertices on surface into a textfile

[Greve, Douglas N.,Ph.D.]

mris_convert lh.white lh.white.asc will convert it to ascii. This file 
will have both xyz coordinates and neighborhood relationships, so you'll 
have to delete the latter. You can also load the surface into matlab 
with read_surf.m

On 10/03/2018 11:48 AM, Sims, Sara A wrote:
>
> External Email - Use Caution
>
> Hello!
>
> I would like to output the location and value of each vertex on a 
> surface to a text file. How could I go about doing this?
>
> Thanks,
>
> Sara Sims
>
>
>
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Re: [Freesurfer] mri_surf2surf --mapmethod nnf not working?

[Greve, Douglas N.,Ph.D.]

Are you worried about where it says "Using surf2surf_nnfr()"? There is actually 
one one function that performs both kinds of mapping. In this case, it is not 
doing the reverse loop. You can reassure yourself by running it with nnfr and 
see that it prints out "Surf2Surf: Reverse Loop" (which does not appear with 
nnf)



On 10/3/18 7:05 PM, Viessmann, Olivia M. wrote:

Hello,


I am using mri_surf2surf and would like to use the vertex map method nnf 
("neighest neighbor, forward only") which according to the --help description 
exists and avoids multiple source vertices to be mapped and averaged onto a 
single target vertex (crucial to my analysis here). However, when I run this 
the output suggests that it is running the nnfr (neighest-neighbor forward and 
reverse) method.

Is this a bug or am I misinterpreting the console output?


This is the command and output:


/usr/local/freesurfer/dev/bin/mri_surf2surf --srcsubject 994273 --sval 
994273/Results/Orientations/lh_SSangle_depth00_rfMRI_REST1_LR.mgz --trgsubject 
fsaverage --mapmethod nnf --o lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz 
--hemi lh

sysname  Linux
machine  x86_64
user omv4
srcsubject = 994273
srcval = 994273/Results/Orientations/lh_SSangle_depth00_rfMRI_REST1_LR.mgz
srctype=
trgsubject = fsaverage
trgval = lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/cluster/olivia/Data/994273/T1w/994273/surf/lh.sphere.reg
Loading source data
Reading target surface reg 
/cluster/olivia/Data/994273/T1w/fsaverage/surf/lh.sphere.reg
Done
Using surf2surf_nnfr()
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 26240
nTrg121 = 163842, nTrgMulti = 0, MnTrgMultiHits = 0
nSrc121 = 78298, nSrcLost = 26240, nSrcMulti = 62974, MnSrcMultiHits = 1.3584
Saving target data
Saving to lh_SSangle_depth00_rfMRI_REST1_LR_inFSAv.mgz



I'd appreciate any suggestions.

Thanks

Olivia





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Re: [Freesurfer] nu_correct disk i/o issues

[Greve, Douglas N.,Ph.D.]

Not that I know of, but this is not a native FS script, it comes from the MNI, 
so it could be doing something we don't understand. Can you do an experiment 
for us? Can you run it outside of the container using reprozip (or something 
equivalent) to see all the files it touches?

On 10/5/18 5:31 AM, Jasper van den Bosch wrote:

External Email - Use Caution

We are trying to run recon_all inside an fmriprep singularity container, but 
are running into an issue with nu_correct. It says it cannot write to disk, 
however there is plenty of space on the tmpdir and output dir. Does this script 
try to write to any other locations? Because this would fail inside the 
container, where each writable location has to be 'mounted'.

Error message:

ncendef: ncid 5: No space left on device
Error outputting volume: possibly disk full?
nu_evaluate: crashed while running evaluate_field (termination status=139)
nu_correct: crashed while running nu_evaluate (termination status=65280)
ERROR: nu_correct

Command ran:

nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc 
./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1121/0/ 
-iterations 1000 -distance 50
[xxx@.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/]
 [2018-10-04 14:59:29] running:
  /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 
-iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 
-distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir 
./tmp.mri_nu_correct.mni.1121/0/ ./tmp.mri_nu_correct.mni.1121/nu0.mnc 
./tmp.mri_nu_correct.mni.1121/nu1.imp


this issue at the fmriprep repo: 
https://github.com/poldracklab/fmriprep/issues/1308
possibly related: https://github.com/freesurfer/freesurfer/issues/462

Many thanks for any advice,
Jasper van den Bosch




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Re: [Freesurfer] Definition of circular label centered on peak vertex

[Greve, Douglas N.,Ph.D.]

you can create a label with just that vertex, then use mri_label2label to 
dilate it, then use mri_segstats specifying the label with --slabel, using beta 
as input (--i), and specifying the output as --avfwf. Run it with --help to get 
more info

On 10/5/18 11:10 AM, Milde, Christopher wrote:

External Email - Use Caution

Dear FS experts


I`m interested in extracting beta values from a FSFAST analysis performed in 
the subject`s native space. The beta values shall be extracted from a circular 
label around the peak vertex.


How can you define a circular label centered on the peak to extract average 
stats (e.g. betas) from that label?


I`m aware how to create mask from the whole clusters in a given ROI saving them 
as labels and extracting stats. However I`m not sure how to define a circular 
mask or label.


Thanks in advance

Chris



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Re: [Freesurfer] FW: RE: error glm-fit-sim

[Greve, Douglas N.,Ph.D.]

were there any clusters that survived?

On 10/8/18 12:12 PM, Caroline Beelen wrote:

External Email - Use Caution
The command:

gop@gop-linux:~/freesurfer$ freeview -f 
$SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
 -viewport 3d

The output:

reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)

The command with a bit less strict significance level:

gop@gop-linux:~/freesurfer$ freeview -f 
$SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
 -viewport 3d

The output:

reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)

(and then it says no more).

Both commands visualize the data, but no clusters are found.
Is this how it should be? Does it mean that there is a problem with reading 
colortables or not?

Best, Caroline

Message: 2
Date: Mon, 1 Oct 2018 17:10:28 +
From: "Greve, Douglas N.,Ph.D." 
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] error glm-fit-sim
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu>>
Content-Type: text/plain; charset="Windows-1252"

What says that? What command are you running? What is the other terminal
output?


On 10/01/2018 04:54 AM, Caroline Beelen wrote:
>
> External Email - Use Caution
>
> Dear FS,
>
> I followed the group analysis page for glm analysis and it worked fine
> until the final step. I?m using version 5.3. After performing
> glm-fit-sim it says ?glm-fit done? (for all files), but when trying to
> open these it says:
>
> ?Reading colortable from annotation file?
>
> Colortable with 1 entries read (originally none)
>
> Colortable with 1 entries read (originally none)
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> Resource temporarily unavailable?
>
> (etc..)
>
> It opens, but nothing is visible and I have the feeling it cannot open
> color files??
>
> MRI glmfit gives positive clusters for some values. I therefore used
> the abs sign for glm-fit-sim.
>
> What might be wrong?
>
> Thanks. Caroline




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Re: [Freesurfer] Mri Convert Help

[Greve, Douglas N.,Ph.D.]

Sorry, there are a lot of things going on down there, it is hard to figure out 
what is happening. It looks like the sourcing of SetUpFreeSurfer.sh is failing 
is that right? Then it looks like the copy (cp) is failing. Then when you run 
mri_convert, it looks like another bash error. It looks like mri_convert is 
trying to unpack it as a diffusion file and that may be what is causing the 
final error. Try
export FS_LOAD_DWI=0


On 10/8/18 9:54 PM, Justin Arnett wrote:



Hello Everyone,
I hope you are doing well!

I am trying to recon-all a DICOM file, for the ultimate hope of being able to 
identify the location of M1 via parcellation. I have successfully been able to 
do so for 2 subjects already, though for some reason I am having a problem with 
the MRI convert stage from the .dcm file to the .nii.gz file. I copied/pasted 
the terminal shell I tried performing above. I am using a Mac (Yosemite 
10.10.5) with FreeSurfer V6.0.0

Further, I think it might be helpful to note that I am a very extreme novice in 
computer science/coding--I have completed recon-all's of 2 subjects by 
following, essentially line-by-line, the "FreeSurfer Download and Install 
Page," and this process was the first time I ever used the terminal shell. (In 
this way, I would absolutely LOVE if anyone might be able to explain where I 
went wrong as simplistically as possible).

Thank you all so much for the help- I hope you have a great start to the week!
- Justin


DBI 05 MRI Convert Error


Justins-Computer:~ justinarnett$ export FREESURFER_HOME=/Applications/freesurfer
Justins-Computer:~ justinarnett$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
-bash: [: /Users/justinarnett: binary operator expected
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
MNI_DIR   /Applications/freesurfer/mni
Justins-Computer:~ justinarnett$ export 
SUBJECTS_DIR=/Applications/freesurfer/subjects/DBI05MRI
Justins-Computer:~ justinarnett$ cd /Applications/freesurfer/subjects/DBI05MRI
Justins-Computer:DBI05MRI justinarnett$ cp 
$FREESURFER_HOME/subjects/DBI05MRI/Image1.dcm
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
   cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... 
target_directory
Justins-Computer:DBI05MRI justinarnett$ mri_convert Image1.dcm Image1.nii.gz
/Applications/freesurfer/FreeSurferEnv.sh: line 226: [: /Users/justinarnett: 
binary operator expected
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
grep: /Users/justinarnett: Is a directory
grep: 1/matlab/startup.m: No such file or directory
mri_convert.bin Image1.dcm Image1.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from Image1.dcm...
Starting DICOMRead2()
dcmfile = /Applications/freesurfer/subjects/DBI05MRI/Image1.dcm
dcmdir = /Applications/freesurfer/subjects/DBI05MRI
Ref Series No = 401
Found 824 files, checking for dicoms
WARNING: tag ImageNumber not found in 
/Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag SeriesNumber not found in 
/Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag image orientation not found in 
/Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
ERROR: GetDICOMInfo(): dcmGetDWIParams() 10
DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
break DICOMRead.c:5228
Found 164 dicom files in series.
WARNING: tag ImageNumber not found in 
/Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag SeriesNumber not found in 
/Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
WARNING: tag image orientation not found in 
/Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
ERROR: GetDICOMInfo(): dcmGetDWIParams() 10
DICOM File: /Applications/freesurfer/subjects/DBI05MRI/DICOMDIR
break DICOMRead.c:5228
First Sorting
Computing Slice Direction
Vs: -120.054 -103.192 34.4639
Vs: -0.741 -0.636922 0.212719
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 165
ndcmfiles = 165
MRIallocSequence(0, 0, 165, 1): bad parm
No such file or directory
ERROR: mri alloc failed



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Re: [Freesurfer] Recon-all with/without T2 give the same stats

[Greve, Douglas N.,Ph.D.]

The aseg.stats should be the same since that does not make reference to the 
surfaces. The aparc stats should have been different because the thickness 
should have been different. Can you check whether the thickness files are 
different?

On 10/8/18 9:39 AM, Jianzhong Chen wrote:

External Email - Use Caution

Dear All,

I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the 
aseg stats and aparc stats with/without T2 are exactly the same. When I check 
the pial surfaces, I can see that they are very similar but not the same. So is 
it reasonable to see exactly the same stats?
An example of the pial surfaces with/without T2 is attached here. The red line 
is lh.pial with T2 and the yellow line is the lh.pial without T2
My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all -T2 
T2.nii -T2pial -sd ${T2_dir}
My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii -all 
-sd ${T1_dir}

Thanks,
Jianzhong



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Re: [Freesurfer] Recon-all with/without T2 give the same stats

[Greve, Douglas N.,Ph.D.]

But are the lh.thickness files the same or different?

On 10/9/18 1:46 AM, Jianzhong Chen wrote:

External Email - Use Caution

Hi Dr. Greve,

I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses (and the other 
measures like volume and area) are all the same.

Thanks,
Jianzhong

Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> 
于2018年10月9日周二 上午10:16写道：
The aseg.stats should be the same since that does not make reference to the 
surfaces. The aparc stats should have been different because the thickness 
should have been different. Can you check whether the thickness files are 
different?

On 10/8/18 9:39 AM, Jianzhong Chen wrote:

External Email - Use Caution

Dear All,

I tried recon-all with/without T2 image using FS 5.3.0. Then I found that the 
aseg stats and aparc stats with/without T2 are exactly the same. When I check 
the pial surfaces, I can see that they are very similar but not the same. So is 
it reasonable to see exactly the same stats?
An example of the pial surfaces with/without T2 is attached here. The red line 
is lh.pial with T2 and the yellow line is the lh.pial without T2
My command for recon-all with T2 is: recon-all -s ${subject} -i T1.nii -all -T2 
T2.nii -T2pial -sd ${T2_dir}
My command for recon-all without T2 is: recon-all -s ${subject} -i T1.nii -all 
-sd ${T1_dir}

Thanks,
Jianzhong



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Re: [Freesurfer] Talairach failed in monkey brain

[Greve, Douglas N.,Ph.D.]

The file passed to --reg should be a registration file. This is a text file 
with the transformation matrix and a few other things, not a volume file.

On 10/8/18 5:28 PM, Frehiwot Woldeyes wrote:

External Email - Use Caution

Hello Freesurfers,

I was attempting to reconstruct a monkey brain, i encountered an error during 
talairach registration step, i have used tkregister2 to manually edit the 
registration but i have gotten error there too:

tkregister2 --targ 
/usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --mov 
/usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii --reg 
/usr/local/freesurfer/subjects/A004_crop.mhd.nii
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii
movable volume /usr/local/freesurfer/subjects/monkey/mri/orig/A04_crop.mhd.nii
reg file   /usr/local/freesurfer/subjects/A004_crop.mhd.nii
LoadVol1
ZeroCRAS   0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
regio_read_register(): No such file or directory
Could not open /usr/local/freesurfer/subjects/A004_crop.mhd.nii
ERROR: reading /usr/local/freesurfer/subjects/A004_crop.mhd.nii

Do you have any thoughts on how to troubleshoot this one?

Regards,
frehiwot



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Re: [Freesurfer] Extract individual vertex thickness values from cortical parcellations

[Greve, Douglas N.,Ph.D.]

You can use matlab. read_curv.m will read in a thickness. 
read_annotation.m will read in the annotation. Look at the help in both 
for more info

On 10/06/2018 11:36 AM, lindsay hanford wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Community,
>
> I am looking for a way to extract thickness values at the level of 
> each vertex from Freesurfer atlas-based parcellated regions 
> (aparc.annot), or more generally lobes. Is this possible?
>
> Using mri_segstats I know it is possible to get more general metrics 
> such as min, max and average thickness values, and # of voxels. Is it 
> possible to use an annot file to read out the raw thickness values?
>
> This post was the closest I could find to answering my question, 
> however, this was at the group level and not specified for parcellated 
> regions. 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022097.html
>
> Thank you in advance,
>
> Lindsay
>
> -- 
> *Lindsay Hanford, PhD*
> *The Buckner Laboratory**|**Harvard University*
>
>
>
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Re: [Freesurfer] nu_correct disk i/o issues

[Greve, Douglas N.,Ph.D.]

BTW, this should not be a problem in the next version

On 10/07/2018 08:29 AM, Jasper van den Bosch wrote:
>
>
> Michael, I can't thank you enough.
>
> Knowing that it writes to /tmp made all the difference.
> In my case I mounted an external directory on /tmp instead of the 
> sessiondir approach, but it now runs fine.
> Jasper
>
> On Fri, 5 Oct 2018 at 23:47, Michael Krause  <mailto:kra...@mpib-berlin.mpg.de>> wrote:
>
> Dear *,
>
> we also run Freesurfer on a cluster and are starting to use
> singularity, so
> naturally I'm curious about this issue.
>
> I was able to reproduce the error with a clean singularity run (-c
> -e).
> Then, I rebuilt a container to start nu_correct with "strace -f -e
> open,write" and I believe I found the problem:
>
> [pid 35994]
> open("/subs/testsub/mri/tmp.mri_nu_correct.mni.35410/nu1.imp",
> O_RDONLY) = 3
> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_EXCL, 0600) = 5
> [pid 35994] open("/tmp/minc-qKdMD4", O_RDWR|O_CREAT|O_TRUNC, 0666) = 5
> [pid 35994] write(5, "\0\0\0\0\0\0\0\0", 8) = 8
> [pid 35994] write(5,
> "CDF\1\0\0\0\0\0\0\0\n\0\0\0\3\0\0\0\6xspace\0\0\0\0\1\0"...,
> 8192) = 8192
> [pid 35994] write(5,
> 
> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"...,
> 8192) = 8192
> [...]
> [pid 35994] write(5,
> 
> "|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0|\360\0\0"...,
> 8192) = -1 ENOSPC (No space left on device)
> [pid 35994] write(2, "ncendef: ", 9ncendef: )    = 9
> [pid 35994] write(2, "ncid 5", 6ncid 5)       = 6
> [pid 35994] write(2, ": No space left on device", 25: No space left on
> device) = 25
>
>
> So there are two issues here I think:
>
> 1) nu_correct is saving things to /tmp when it could just use ./tmp
> 2) the singularity default for "sessiondir max size" is 16MB,
> which includes
> /tmp, is too small for the minc-tmp files
>
> I changed the value from 16 to 1024 and it passed the nu_correct step.
>
> cheers,
> Michael
>
> On 10/5/18 5:57 PM, Greve, Douglas N.,Ph.D. wrote:
> > Not that I know of, but this is not a native FS script, it comes
> from the
> > MNI, so it could be doing something we don't understand. Can you
> do an
> > experiment for us? Can you run it outside of the container using
> reprozip
> > (or something equivalent) to see all the files it touches?
> >
> > On 10/5/18 5:31 AM, Jasper van den Bosch wrote:
> >>
> >> External Email - Use Caution
> >>
> >> We are trying to run recon_all inside an fmriprep singularity
> container,
> >> but are running into an issue with nu_correct. It says it
> cannot write to
> >> disk, however there is plenty of space on the tmpdir and output
> dir. Does
> >> this script try to write to any other locations? Because this
> would fail
> >> inside the container, where each writable location has to be
> 'mounted'.
> >>
> >> Error message:
> >>
> >> ncendef: ncid 5: No space left on device
> >> Error outputting volume: possibly disk full?
> >> nu_evaluate: crashed while running evaluate_field (termination
> status=139)
> >> nu_correct: crashed while running nu_evaluate (termination
> status=65280)
> >> ERROR: nu_correct
> >>
> >> Command ran:
> >>
> >> nu_correct -clobber ./tmp.mri_nu_correct.mni.1121/nu0.mnc
> >> ./tmp.mri_nu_correct.mni.1121/nu1.mnc -tmpdir
> >> ./tmp.mri_nu_correct.mni.1121/0/ -iterations 1000 -distance 50
> >> [xxx@.cluster:/data/BIDS/derivatives/freesurfer/sub-1/mri/]
> >> [2018-10-04 14:59:29] running:
> >>   /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
> -sharpen 0.15
> >> 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask
> -nonotify -b_spline
> >> 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir
> >> ./tmp.mri_nu_correct.mni.1121/0/
> ./tmp.mri_nu_correct.mni.1121/nu0.mnc
> >> ./tmp.mri_nu_correct.mni.1121/nu1.imp
> >>
> >>
> >> this issue at the fmriprep
> >> repo: https://github.com/poldracklab/fmriprep/issues/1308
> >> pos

Re: [Freesurfer] masking cortical thickness

[Greve, Douglas N.,Ph.D.]

Use the --outmask option

On 10/07/2018 08:59 AM, N Saf wrote:
>
> External Email - Use Caution
>
> Dear Douglos,
>
> I did not understand how to use mri_label2label with the mask 
> option(there is srcmask options not mask alone !). I extract my labels 
> and as you explained I wanted to create i.e. binary mask of 
> rh.fusiform.label  with mri_label2label :
>   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label 
> --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface 
> --hemi rh
>
> but it creats another label file not binary with mgh format I did not 
> get how can I create mybinary.mgh mask in order to use in third 
> command "mri_binarize --i lh.thickness --mask youmask.mgh --o 
> lh.thickness.masked.mgh"
>
> would you please help me with this, it would be a great favor.
>
> Best regards,
> Nazanin
>
> On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Yes, that should work. You can create a mask by breaking the
> annotation
> into labels (mri_annotation2label), then converting the label into a
> binary mask (mri_label2label with --mask option), then
> mri_binarize --i
> lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
>
>
> On 07/30/2018 01:47 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer Experts,
> >
> > I wonder how can I show the cortical thickness surface on just one
> > region of my interest in Freeview.  assume that I want to see the
> > thickness surface of one of the regions in DKTatlas. does it
> work if I
> > make a binary mask of that specific region on
> aparcDKTatlas.annot and
> > then multiply it to the ?h.thickness surface ?? any help will be
> > appreciated.
> >
> > Best Regards,
> > Nazanin
> >
> >
> > ___
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> 
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> whom it is
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> contains patient information, please contact the Partners
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Re: [Freesurfer] masking cortical thickness

[Greve, Douglas N.,Ph.D.]

if you want to mask the thickness, then use mri_mask

On 10/10/2018 10:30 AM, N Saf wrote:
>
> External Email - Use Caution
>
> Dear Douglos,
>
> as you recommended, I used the --outmask and create the binary mask of 
> a label in mgh format. as I use the mri_binarize command with this 
> mask and ?h.thickness; the output is binary too or if I use --match 
> flag or --min --max flag the out put is 1 for those range, but I want 
> the thickness values on my mask, not 1 all over it , how should I do that?
>
> any detail information will be appreciated.
>
> BRG,
> Nazanin
>
>
> On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Use the --outmask option
>
> On 10/07/2018 08:59 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Douglos,
> >
> > I did not understand how to use mri_label2label with the mask
> > option(there is srcmask options not mask alone !). I extract my
> labels
> > and as you explained I wanted to create i.e. binary mask of
> > rh.fusiform.label  with mri_label2label :
> >   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label
> > --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface
> > --hemi rh
> >
> > but it creats another label file not binary with mgh format I
> did not
> > get how can I create mybinary.mgh mask in order to use in third
> > command "mri_binarize --i lh.thickness --mask youmask.mgh --o
> > lh.thickness.masked.mgh"
> >
> > would you please help me with this, it would be a great favor.
> >
> > Best regards,
> > Nazanin
> >
> > On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve
> > mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>
> wrote:
> >
> >     Yes, that should work. You can create a mask by breaking the
> >     annotation
> >     into labels (mri_annotation2label), then converting the
> label into a
> >     binary mask (mri_label2label with --mask option), then
> >     mri_binarize --i
> >     lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
> >
> >
> >     On 07/30/2018 01:47 AM, N Saf wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Dear Freesurfer Experts,
> >     >
> >     > I wonder how can I show the cortical thickness surface on
> just one
> >     > region of my interest in Freeview.  assume that I want to
> see the
> >     > thickness surface of one of the regions in DKTatlas. does it
> >     work if I
> >     > make a binary mask of that specific region on
> >     aparcDKTatlas.annot and
> >     > then multiply it to the ?h.thickness surface ?? any help
> will be
> >     > appreciated.
> >     >
> >     > Best Regards,
> >     > Nazanin
> >     >
> >     >
> >     > ___
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> >
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> >
> >
> >     The information in this e-mail is intended only for the
> person to
> >     whom it is
> >     addressed. If you believe this e-mail was sent to you in
> error and
> >     the e-mail
> >     contains patient information, please contact the Partners
> >     Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
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> >     sender and properly
> >   

Re: [Freesurfer] Difference between 2 mgh files in surf dir (or: effects of 'mri_surf2surf --prune' without smoothing)

[Greve, Douglas N.,Ph.D.]

I think they are probably the same thing. Can you run
mri_diff lh.area.fsaverage.mgh lh.area.fwhm0.fsaverage.mgh



On 10/10/2018 11:12 AM, ts...@rcmd.org wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> what is the difference between the following 2 files found in a subject's 
> surf/ directory:
>* file #1: lh.area.fsaverage.mgh
>* file #2: lh.area.fwhm0.fsaverage.mgh
>
>
> I see in the logs (/scripts/recon-all.log), that file #2 is 
> generated from file #1 by running the following command:
>
>  mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval 
> lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex
>
> I know that if fwhm > 0, spatial smoothing will be applied. But what happens 
> if fwhm is 0? From a quick comparison of the data in both files, they seem to 
> be identical, but the hashes of the files differ. Is the difference only 
> about the header?
>
> Thanks for your help,
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
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Re: [Freesurfer] Pet Surfer

[Greve, Douglas N.,Ph.D.]

Is this for an ROI-based study or a map-based study? For ROI, we use the 
GTM, and it PV corrects for all structures (including WM and CSF). For 
map-based, we use MG. MG removes WM (and CSF) entirely. In theory, it 
can be run in a way to keep WM and throw GM and CSF away, but that is 
not implemented. Does this answer your questions?



On 10/10/2018 07:31 AM, David.Mackarthy wrote:
>
>
> Dear Dr Greeve,
> I am following petsurfer pipeline to do surface based analysis of 
> PET-FDG data and I have interest in doing partial volume correction. I 
> would like to inquire about:
>
> 1) Can partial volume correction be applied on white mater, or just on 
> gray matter?
>
> 2) Can partial volume correction be applied between gray matter and CSF?
>
> According to Muller-Gartner (MG) Method we segment the brain to 
> gray/white and csf, then we apply partial volume correction only on 
> gray matter. why not on the other parts.
>
> I apologies if my question is basics and I appreciate your input.
>
> Thanks for publishing this valuable manuscript
>
> https://www.ncbi.nlm.nih.gov/pubmed/26915497
>
> With all respect!
> Dev
>
>
>
>
>
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Re: [Freesurfer] Recon-all with/without T2 give the same stats

[Greve, Douglas N.,Ph.D.]

I think this was a bug in 5.3. Try running recon-all like
recon-all -s subject -parcstats -parcstats2 -parcstats3
to regenerate the stats files

On 10/09/2018 11:19 PM, Jianzhong Chen wrote:
>
> External Email - Use Caution
>
> They are different. I attached two screenshots of lh.thickness 
> overlaying on lh.inflated here.
>
> Greve, Douglas N.,Ph.D.  <mailto:dgr...@mgh.harvard.edu>> 于2018年10月9日周二 下午10:22写道：
>
> But are the lh.thickness files the same or different?
>
> On 10/9/18 1:46 AM, Jianzhong Chen wrote:
>>
>> External Email - Use Caution
>>
>> Hi Dr. Greve,
>>
>> I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses
>> (and the other measures like volume and area) are all the same.
>>
>> Thanks,
>> Jianzhong
>>
>> Greve, Douglas N.,Ph.D. > <mailto:dgr...@mgh.harvard.edu>> 于2018年10月9日周二 上午10:16写道：
>>
>> The aseg.stats should be the same since that does not make
>> reference to the surfaces. The aparc stats should have been
>> different because the thickness should have been different.
>> Can you check whether the thickness files are different?
>>
>> On 10/8/18 9:39 AM, Jianzhong Chen wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Dear All,
>>>
>>> I tried recon-all with/without T2 image using FS 5.3.0. Then
>>> I found that the aseg stats and aparc stats with/without T2
>>> are exactly the same. When I check the pial surfaces, I can
>>> see that they are very similar but not the same. So is it
>>> reasonable to see exactly the same stats?
>>> An example of the pial surfaces with/without T2 is attached
>>> here. The red line is lh.pial with T2 and the yellow line is
>>> the lh.pial without T2
>>> My command for recon-all with T2 is: recon-all -s ${subject}
>>> -i T1.nii -all -T2 T2.nii -T2pial -sd ${T2_dir}
>>> My command for recon-all without T2 is: recon-all -s
>>> ${subject} -i T1.nii -all -sd ${T1_dir}
>>>
>>> Thanks,
>>> Jianzhong
>>>
>>>
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Re: [Freesurfer] error glm-fit-sim (message 11)

[Greve, Douglas N.,Ph.D.]

Probably so

On 10/10/2018 03:41 AM, Caroline Beelen wrote:
>  External Email - Use Caution
>
> Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when 
> visualizing). However, I'm not sure if I should also see this in a text file. 
> Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no 
> clusters. At least, under the line ClusterNo Max VtxMax Size MNIX MNIY etc. 
> nothing is written.
>
> But does a lack of significant clusters also explain the weird messages of 
> "colortable with 1 entries read (originally none)" (& "CTABisEntryValid: 
> index -1 was OOB" & "Resource temporarily unavailable") that show up in the 
> terminal?
>
> Thanks very much, Caroline
>
>
>
> -Oorspronkelijk bericht-
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens 
> freesurfer-requ...@nmr.mgh.harvard.edu
> Verzonden: dinsdag 9 oktober 2018 18:00
> Aan: freesurfer@nmr.mgh.harvard.edu
> Onderwerp: Freesurfer Digest, Vol 176, Issue 9
>
> Send Freesurfer mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. FW: RE: error glm-fit-sim (Caroline Beelen)
> 2. Re: output values of vertices on surface into atextfile
>(Sims, Sara A)
> 3. Re: output values of vertices on surface into a textfile
>(Bruce Fischl)
> 4. Re: output values of vertices on surface into atextfile
>(Sims, Sara A)
> 5. Re: Hippocampal segmentation with an additional scan ERROR
>kvlGEMSMatlab (Pradeep)
> 6. Re: Hippocampal segmentation with an additional scan ERROR
>kvlGEMSMatlab (Iglesias Gonzalez, Eugenio)
> 7. hippocampal subfields (Marcel Heers)
> 8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio)
> 9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert)
>10. Talairach failed in monkey brain (Frehiwot Woldeyes)
>    11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.)
>12. Mri Convert Help (Justin Arnett)
>13. Re: Mri Convert Help (Greve, Douglas N.,Ph.D.)
>14. Re: Recon-all with/without T2 give the same stats
>(Greve, Douglas N.,Ph.D.)
>15. Re: Recon-all with/without T2 give the same stats (Jianzhong Chen)
>16. m.khalil...@sutech.ac.ir sent you files via WeTransfer
>    (WeTransfer)
>17. very bad result using "mris_ca_train" and  "mris_ca_label"
>(Maedeh Khalilian)
>18. Re: Talairach failed in monkey brain (Greve, Douglas N.,Ph.D.)
>    19. Re: Recon-all with/without T2 give the same stats
>    (Greve, Douglas N.,Ph.D.)
>20. Re: very bad result using "mris_ca_train" and "mris_ca_label"
>(Bruce Fischl)
>21. Re: Extract individual vertex thickness values from cortical
>parcellations (Greve, Douglas N.,Ph.D.)
>22. Re: nu_correct disk i/o issues (Greve, Douglas N.,Ph.D.)
>23. Re: masking cortical thickness (Greve, Douglas N.,Ph.D.)
>
>
> --
>
> Message: 1
> Date: Mon, 8 Oct 2018 16:12:06 +
> From: Caroline Beelen 
> Subject: [Freesurfer] FW: RE: error glm-fit-sim
> To: "freesurfer-boun...@nmr.mgh.harvard.edu"
>   ,
>   "freesurfer@nmr.mgh.harvard.edu"
> Message-ID:
>   <4051d561c94b40e0b641202b7bad7...@icts-s-exmbx25.luna.kuleuven.be>
> Content-Type: text/plain; charset="us-ascii"
>
>  External Email - Use Caution
>
> The command:
>
> gop@gop-linux:~/freesurfer$ freeview -f 
> $SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
>  -viewport 3d
>
> The output:
>
> reading colortable from annotation file...
> colortable with 1 entries read (originally none)
> colortable with 1 entries read (originally none)
> CTABisEntryValid: index -1 was OOB
> Resource temporarily unavailable
> Resource temporarily unavailable
> B
> ginally none)
> CTABisEntryValid: index -1 was OOB

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Greve, Douglas N.,Ph.D.]

Which subject did you load it on? It must be fsaverage. Can you send the 
terminal output and command line?

On 10/03/2018 11:31 PM, Ting Li wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Expert,
>
> I have figured out the problem is that I didn’t specify lh before the 
> annot file. However, in this method, I didn’t get the right label for 
> I have loaded the label into the subject file. It is the scatter points.
>
> I want to create label through mri_glm-fit-sim clusters. What command 
> I should use? Please specify it for me. Thanks a lot!
>
> Your help means a lot.
>
> Regards,
> Ting
>> On Oct 3, 2018, at 9:38 PM, Ting Li > > wrote:
>>
>> I have also tried the command without annot in specifying the 
>> annotation file. Thanks a lot.
>>
>> Regards,
>>
>> Ting
>>> On Oct 3, 2018, at 9:36 PM, Ting Li >> > wrote:
>>>
>>> Dear Freesurfer Experts,
>>>
>>> I really need your attention and help. Thanks a lot.
>>>
>>> We want to create label through the mri_glm-fit-sim cluster results.
>>>
>>> We have found the same topic in 2013 and tried the method you have 
>>> provided. However, it doesn’t work. If you think it is not the right 
>>> way, could you give me an example to do it right. I really 
>>> appreciate your great help. Thanks a lot.
>>>
>>> Here is my code:
>>>
>>> mri_annotation2label --subject F999  --hemi lh --annotation 
>>> cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
>>>
>>> Here is my error information:
>>> subject = F999
>>> annotation = cache.th20.neg.sig.ocn.annot
>>> hemi = lh
>>> labelbase = lh.test_label
>>> surface   = white
>>>
>>> Reading surface
>>>  /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
>>> Loading annotations from 
>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>>> could not read annot file 
>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>>> No such file or directory
>>> INFO: could not load from 
>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
>>>  
>>> trying 
>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>>> could not read annot file 
>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>>> No such file or directory
>>> ERROR: MRISreadAnnotation() failed
>>>
>>> This is the annot files in my directory F999:
>>> ls F999/label/*.annot
>>> F999/label/cache.th20.neg.sig.ocn.annot 
>>> F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
>>> F999/label/lh.aparc.a2009s.annot 
>>> F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
>>> F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot 
>>> F999/label/rh.BA_exvivo.thresh.annot
>>> F999/label/lh.aparc.DKTatlas.annot       F999/label/rh.aparc.annot
>>
>
>
>
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Re: [Freesurfer] Moving VOI to FreeSurfer Space

[Greve, Douglas N.,Ph.D.]

what do you mean by FreeSurfer space?

On 10/02/2018 10:11 AM, Sarosh, Cyrus wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Experts,
>
> I’m trying to find the best method and command to move a hand drawn 
> VOI in original MRI space to FreeSurfer space. These scans have 
> already been ran through the entire FreeSurfer process and the hand 
> drawn VOIs have already been converted to .mgz files. Thanks for your help
>
> Thanks,
>
> Cyrus
>
> Cyrus Sarosh
>
> Description: Description: Description: Description: Description: 
> Description: Description: cid:image002.png@01CC3BB7.F8D9A990
>
> Research Area Specialist Associate
>
> Department of Radiology
>
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>
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>
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>
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>
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>
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Re: [Freesurfer] Pet Surfer

[Greve, Douglas N.,Ph.D.]

It could make sense to apply it to WM. CSF I'm not so sure. Are you 
really trying to measure the signal in CSF?

On 10/10/18 6:08 PM, David.Mackarthy wrote:
>  External Email - Use Caution
>
> Dear Dr Greve, thank you for the response
> This is for a map-based study. Absolutely, this is clear, I appreciate the 
> response. I just have one additional question and I appreciate your patience.
>
> Is it recommended to apply PVC on white matter or csf? does it make sense to 
> apply PVC on WM and CSF?
>
> Thank you so much!
>
>
>
> ‐‐‐ Original Message ‐‐‐
> On Wednesday, October 10, 2018 2:17 PM, Greve, Douglas N.,Ph.D. 
>  wrote:
>
>> Is this for an ROI-based study or a map-based study? For ROI, we use the
>> GTM, and it PV corrects for all structures (including WM and CSF). For
>> map-based, we use MG. MG removes WM (and CSF) entirely. In theory, it
>> can be run in a way to keep WM and throw GM and CSF away, but that is
>> not implemented. Does this answer your questions?
>>
>> On 10/10/2018 07:31 AM, David.Mackarthy wrote:
>>
>>> Dear Dr Greeve,
>>> I am following petsurfer pipeline to do surface based analysis of
>>> PET-FDG data and I have interest in doing partial volume correction. I
>>> would like to inquire about:
>>>
>>> 1.  Can partial volume correction be applied on white mater, or just on
>>>  gray matter?
>>>
>>> 2.  Can partial volume correction be applied between gray matter and CSF?
>>>
>>>
>>> According to Muller-Gartner (MG) Method we segment the brain to
>>> gray/white and csf, then we apply partial volume correction only on
>>> gray matter. why not on the other parts.
>>> I apologies if my question is basics and I appreciate your input.
>>> Thanks for publishing this valuable manuscript
>>> https://www.ncbi.nlm.nih.gov/pubmed/26915497
>>> With all respect!
>>> Dev
>>>
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space

[Greve, Douglas N.,Ph.D.]

I'm not sure what you are trying to do. Do you want to map the vbm 
results to the surface and visualize the aparc (desikan atlas) or do you 
want to map the aparc into the vbm volume?

On 10/11/2018 09:59 AM, ece ulug wrote:
>
> External Email - Use Caution
>
> Hi,
>
> May be i cannot tell well,
>
>
> I would like to use the Desikan atlas, which is a surface-based atlas 
> normally, as a volume template.
>
> Generally Desikan_surface.gii file is accesible. Can I visualize VBM 
> results correctly in for instances SPMglass brain using Desikan Atlas.nii?
>
>
> Ece
>
>
> 
> *Gönderen:* ece ulug 
> *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27
> *Kime:* freesurfer@nmr.mgh.harvard.edu
> *Konu:* Desikan Atlas in MNI Space
>> /Dear All,/
>> /
>> I am a master student in Turkey. For my thesis; I have to do exactly 
>> this;
>>
>> /
>> /*Desikan atlas (which I have in the tailarach space) in the MNI 
>> space, as a file (Desikan_mni.nii). I am aware that transforming from 
>> one space to the other is not a very good idea but nevertheless I 
>> would like to test some computations.
>>
>> Anyone can attach/send a link/know of if exists such a file? the 
>> aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
>> */
>> /This is a mail dated 2014, freesurfer maillist, and I find this via 
>> internet./
>> /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for 
>> these file? /
>> /And what is your opinion, is it good idea? /
>> /(To transform Desikan atlas to mni space for visualization VBM 
>> results?) /
>> /Thanks in advance/
>> /E. Ece Uluğ/
>
>
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Re: [Freesurfer] mri_watershed Error

[Greve, Douglas N.,Ph.D.]

can you send the recon-all log file?

On 10/11/2018 11:22 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> When I run recon-all i get the follwing error message:
>
>  mri_watershed Error:
>  GLOBAL region of the brain empty !
> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 
> 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018
>
> The .nii file looks fine. Can someone help me with this?
>
> Best,
> Boris
>
>
>
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Re: [Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

[Greve, Douglas N.,Ph.D.]

Which template surface? fsaverage? Are you using the 2mm MNI template 
for VBM?  If so, then you can use mri_label2vol specifying the desikan 
annotation as the --annot and using 
$FREESURFER_HOME/average/mni152.register.dat as the registration file.

On 10/11/2018 11:42 AM, ece ulug wrote:
>
> External Email - Use Caution
>
> Thanks for your response;
>
>
> I had already mapped normalized volume to template surface, so now I 
> want to map the desikan atlas into the vbm volume.
>
>
>
> ----------------
> *Gönderen:* Greve, Douglas N.,Ph.D.  adına 
> freesurfer-boun...@nmr.mgh.harvard.edu 
> 
> *Gönderildi:* 11 Ekim 2018 Perşembe 18:26
> *Kime:* freesurfer@nmr.mgh.harvard.edu
> *Konu:* Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space
> I'm not sure what you are trying to do. Do you want to map the vbm
> results to the surface and visualize the aparc (desikan atlas) or do you
> want to map the aparc into the vbm volume?
>
> On 10/11/2018 09:59 AM, ece ulug wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > May be i cannot tell well,
> >
> >
> > I would like to use the Desikan atlas, which is a surface-based atlas
> > normally, as a volume template.
> >
> > Generally Desikan_surface.gii file is accesible. Can I visualize VBM
> > results correctly in for instances SPMglass brain using Desikan 
> Atlas.nii?
> >
> >
> > Ece
> >
> >
> > 
> > *Gönderen:* ece ulug 
> > *Gönderildi:* 10 Ekim 2018 Çarşamba 12:27
> > *Kime:* freesurfer@nmr.mgh.harvard.edu
> > *Konu:* Desikan Atlas in MNI Space
> >> /Dear All,/
> >> /
> >> I am a master student in Turkey. For my thesis; I have to do exactly
> >> this;
> >>
> >> /
> >> /*Desikan atlas (which I have in the tailarach space) in the MNI
> >> space, as a file (Desikan_mni.nii). I am aware that transforming from
> >> one space to the other is not a very good idea but nevertheless I
> >> would like to test some computations.
> >>
> >> Anyone can attach/send a link/know of if exists such a file? the
> >> aparc+aseg.mgz in fsaverage is in mni305 space. will that work?
> >> */
> >> /This is a mail dated 2014, freesurfer maillist, and I find this via
> >> internet./
> >> /Desikan Atlas 'aparc+aseg.mgz' or .nii format where should I look for
> >> these file? /
> >> /And what is your opinion, is it good idea? /
> >> /(To transform Desikan atlas to mni space for visualization VBM
> >> results?) /
> >> /Thanks in advance/
> >> /E. Ece Uluğ/
> >
> >
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Greve, Douglas N.,Ph.D.]

yes, that is fine

On 10/11/18 11:21 PM, Ting Li wrote:

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much for your response. With your instruction, it works. This is 
how I did.

First, copy the significant cluster annot file from the simulation fold to one 
of subject label folder.
Secondly, use the mir_annotation2label command to make this cluster into a 
label file
Thirdly, copy this label file to fsaverage label folder
Finally, I can load the label to the fsaverage surf.

Is this the right procedure? Thanks a lot!

Regards,
Ting
On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:

Which subject did you load it on? It must be fsaverage. Can you send the
terminal output and command line?

On 10/03/2018 11:31 PM, Ting Li wrote:

External Email - Use Caution

Dear Freesurfer Expert,

I have figured out the problem is that I didn’t specify lh before the
annot file. However, in this method, I didn’t get the right label for
I have loaded the label into the subject file. It is the scatter points.

I want to create label through mri_glm-fit-sim clusters. What command
I should use? Please specify it for me. Thanks a lot!

Your help means a lot.

Regards,
Ting
On Oct 3, 2018, at 9:38 PM, Ting Li mailto:tx...@ualr.edu>
<mailto:tx...@ualr.edu>> wrote:

I have also tried the command without annot in specifying the
annotation file. Thanks a lot.

Regards,

Ting
On Oct 3, 2018, at 9:36 PM, Ting Li mailto:tx...@ualr.edu>
<mailto:tx...@ualr.edu>> wrote:

Dear Freesurfer Experts,

I really need your attention and help. Thanks a lot.

We want to create label through the mri_glm-fit-sim cluster results.

We have found the same topic in 2013 and tried the method you have
provided. However, it doesn’t work. If you think it is not the right
way, could you give me an example to do it right. I really
appreciate your great help. Thanks a lot.

Here is my code:

mri_annotation2label --subject F999  --hemi lh --annotation
cache.th20.neg.sig.ocn.annot --labelbase lh.test_label

Here is my error information:
subject = F999
annotation = cache.th20.neg.sig.ocn.annot
hemi = lh
labelbase = lh.test_label
surface   = white

Reading surface
 /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
Loading annotations from
/media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
could not read annot file
/media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
No such file or directory
INFO: could not load from
/media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
trying
/media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
could not read annot file
/media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
No such file or directory
ERROR: MRISreadAnnotation() failed

This is the annot files in my directory F999:
ls F999/label/*.annot
F999/label/cache.th20.neg.sig.ocn.annot
F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
F999/label/lh.aparc.a2009s.annot
F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot
F999/label/rh.BA_exvivo.thresh.annot
F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot




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Re: [Freesurfer] FreeSurfer Errors

[Greve, Douglas N.,Ph.D.]

On 10/11/18 1:58 PM, Sparsh Jain wrote:

External Email - Use Caution

Hey!

I have recently started using FreeSurfer. I have encountered multiple errors 
over the past few days, and I would like to mention them all.

1. While testing the installation, the code ran for roughly 4-6 hours and 
generated the T1 and wm output images. The brainmask image failed to load even 
after multiple attempts.
what does "failed to load" mean? Please be more specific, supplying command 
lines and terminal output
2. We have patient data from a Seimens 1.5 T MRI machine. They are DICOM images 
(about 120-145 images). Running dcmunpack on the directory to locate the 
suitable T1 weighted image (to pass as the input image to freesurfer) returns 
an error message 'Element not found'. It fails to generate a list of usable 
input images. The log file also only mentions the error message. Basically, I 
am having trouble working with DICOM images using Freesurfer. Please advise me 
on how to go about it.
This usually means that some part of the DICOM that dcmunpack expects is not 
there. Again, command line and terminal output would be helpful.
3. I tried using the dcm2nii tool on the DICOM images. The software gave out 
three (nearly identical) nii.gz files as output, each about 7 MB in size. I 
tried running reconstruction on all three one by one. Only the 'compressed' 
version output underwent reconstruction for a long time without giving any 
errors. However, the reconstruction process went on for 150 hours without 
completion. There were no errors during this time, and the mris_fix_topo 
process went on for about 74 hours until tonight. It was working on 'correcting 
defect 48' for most of this time, and then the PC suddenly stopped responding. 
The process had been utilizing 100% of the CPU and 87% of the RAM for a long 
time, but the computer was always responding. However it suddenly stopped 
responding after about 74 hours of mris_fix_topology process. My machine has 8 
GB RAM and more than 3.4 GHz processing speed (Acer Veriton).
I don't know what is going on here. Did you look at the nii.gz file in freeview 
to make sure that it looks ok. What is the size of the volume?
4. Previously, I tried running reconstruction on a different subject's data 
after converting it to nifti using dcm2niix. After 70 hours of execution, it 
terminated with an error which showed that the fsaverage folder was 
inaccessible. Further digging revealed that the folder  was somehow pointing to 
itself. The original error said failed to read from the label file.
 I had to eventually reinstall FreeSurfer.
I don't know how that happened.
5. I tried running iElvis pipeline. After some time I got an error which said 
that the sphere.reg file couldn't be opened. I tried fixing this but nothing 
worked. I kept getting the error that lh.sphere.reg file could not be opened 
and so on.
I don't know anything about iElvis

Please help. I have been trying to run it for weeks now. I hope you will be 
able to address each of these problems soon.

Thank You

Sparsh



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Re: [Freesurfer] qdec analysis with more than 2 covariates

[Greve, Douglas N.,Ph.D.]

You cannot use QDEC. For this case you'll need to use the "command line" 
stream. You'll need to start by creating an FSGD file
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

On 10/15/18 10:15 AM, vittal korann wrote:

External Email - Use Caution

Hi Doug,

Recently I started working on freesurfer for volume based analysis. For QDEC, I 
need to include more than 2 variables. For example if I include patients who 
hail from different places like statutory town, census town and rural. In 
present scenario, can I include all three as covariates.
Here is the error that qdec showing while running GLM:

"ERROR: Subject 2 seems to have a mismatched number of discrete factors 
(expected 4, found 1)"
"Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified."
"Error in Analyze: command fai;ed mri_glmfit --y
/usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd
/usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir
/usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label"

Could you help us out in this regard.

Would appreciate any help!!

Korann






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Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Greve, Douglas N.,Ph.D.]

Not sure. Can you use mris_convert to convert the asc back to a curv file?

On 10/15/2018 11:20 AM, Worker, Amanda wrote:
>
> External Email - Use Caution
>
> Hello,
>
>
> I am trying to overlay a .asc file in either freeview or tksurfer, but 
> so far having no luck.
>
>
> As practice and to determine the right format, I am simply using 
> lh.thickness, which I've converted to .asc using the following command:
>
>
> % mris_convert -c lh.thickness lh.white lh.thickness.asc
>
>
> I am trying to overlay this onto lh.pial for one subject, however I 
> cannot load the file and I get the following error message:
>
>
> % mri_read(): couldn't determine type of file 
> /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
> surfer: couldn't load 
> /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc.
>  If you were trying to load a functional volume, make sure
> you selected the right registration method, and if necessary,
> that the registration file exists.
> If you were trying to load a volume-encoded value file,
> make sure it has the same number of values as this surface
> does vertices (128970).
> sclv_read_from_volume: error in FunD_New
>
> Interestingly, I can load the file as a curvature file, but then can't 
> play around with the threshold.
>
>
> Do you have any idea what I'm doing wrong? Any help would be appreciated!
>
>
> Thanks,
>
>
> Amanda
>
>
>
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Greve, Douglas N.,Ph.D.]

Click on the surface file name in the upper left corner of FreeView, 
then load the Annotation from the panel just below it. It does not make 
sense that you would see the branches on the folded surface but not on 
the inflated.

On 10/15/2018 03:06 PM, Ting Li wrote:
>
> External Email - Use Caution
>
> I didn't load the annot file. I just use the annot file to create the 
> label. if I check the clusters in a inflated brain, they are looks 
> fine. If I need to load annot file for checking, how can I do it? 
> Thanks a lot.
>
> Ting
>
> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> does the same thing happen when you load the annot file?
>
> On 10/13/18 10:03 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>>
>> Dear Dr. Douglas,
>>
>> I can load the label, but some clusters have branches. Some of
>> them are just looks fine. Do you know the reason? Thanks a lot.
>>
>> Regards,
>> Ting
>>
>>
>>
>>
>>> On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>
>>> yes, that is fine
>>>
>>> On 10/11/18 11:21 PM, Ting Li wrote:
>>>>
>>>> External Email - Use Caution
>>>>
>>>> Dear Dr. Douglas,
>>>>
>>>> Thank you so much for your response. With your instruction, it
>>>> works. This is how I did.
>>>>
>>>> First, copy the significant cluster annot file from the
>>>> simulation fold to one of subject label folder.
>>>> Secondly, use the mir_annotation2label command to make this
>>>> cluster into a label file
>>>> Thirdly, copy this label file to fsaverage label folder
>>>> Finally, I can load the label to the fsaverage surf.
>>>>
>>>> Is this the right procedure? Thanks a lot!
>>>>
>>>> Regards,
>>>> Ting
>>>>> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
>>>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>>
>>>>> Which subject did you load it on? It must be fsaverage. Can
>>>>> you send the
>>>>> terminal output and command line?
>>>>>
>>>>> On 10/03/2018 11:31 PM, Ting Li wrote:
>>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Dear Freesurfer Expert,
>>>>>>
>>>>>> I have figured out the problem is that I didn’t specify lh
>>>>>> before the
>>>>>> annot file. However, in this method, I didn’t get the right
>>>>>> label for
>>>>>> I have loaded the label into the subject file. It is the
>>>>>> scatter points.
>>>>>>
>>>>>> I want to create label through mri_glm-fit-sim clusters. What
>>>>>> command
>>>>>> I should use? Please specify it for me. Thanks a lot!
>>>>>>
>>>>>> Your help means a lot.
>>>>>>
>>>>>> Regards,
>>>>>> Ting
>>>>>>> On Oct 3, 2018, at 9:38 PM, Ting Li >>>>>> <mailto:tx...@ualr.edu>
>>>>>>> <mailto:tx...@ualr.edu>> wrote:
>>>>>>>
>>>>>>> I have also tried the command without annot in specifying the
>>>>>>> annotation file. Thanks a lot.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Ting
>>>>>>>> On Oct 3, 2018, at 9:36 PM, Ting Li >>>>>>> <mailto:tx...@ualr.edu>
>>>>>>>> <mailto:tx...@ualr.edu>> wrote:
>>>>>>>>
>>>>>>>> Dear Freesurfer Experts,
>>>>>>>>
>>>>>>>> I really need your attention and help. Thanks a lot.
>>>>>>>>
>>>>>>>> We want to create label through the mri_glm-fit-sim cluster
>>>>>>>> results.
>>>>>>>>
>>>>>>>> We have found the same topic in 2013 and tried the method
>>&g

Re: [Freesurfer] FreeSurfer Errors (2)

[Greve, Douglas N.,Ph.D.]

can you send the command-line output as text?

On 10/16/2018 11:12 AM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Hey!
> I sent two responses on Friday. The second response was bigger than 1 
> MB so it awaited moderator approval. I don't know if you received it 
> eventually.
>
> Following up to that mail, my reconstruction on the subject with 176 
> images crashed after about 32 hours of execution with the error 'could 
> not read label' and 'too many symbolic links' in fsaverage. I have 
> attached the entire command line output. Please help me understand 
> what I'm doing wrong !
>
> Thanks
>
> Sparsh
>
>
>
>
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Re: [Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation

[Greve, Douglas N.,Ph.D.]

When you look at the vertex in matlab, are you correctly accounting for 
the fact that FreeView uses 0-based indexing and matlab uses 1-based? 
Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be 
using 234740 in matlab below

On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I'm trying to make a surface file from a subject's head and to map 
> coordinates to that surface.  If I run:
>
>
> mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol 
> $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 
> 20 --nhitsmin 2
>
> mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 
> $SUBJECTS_DIR/$sub/surf/lh.seghead
>
> and then load lh.seghead in FreeView, it looks as I would expect.  
> Clicking anywhere near a vertex gives the typical output, showing the 
> closest vertex.  All fine and well. However, if I load the file in Matlab:
>
>
> vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
>
>
> my values are nothing near what I'm seeing in Freeview.  For example, 
> FreeView reports:
>
>
> vertex 234741 [-78.50,14.50,26.50]
>
>
> read_surf reports:
>
>
> vertex 234740 0168.98000
>
> Of note, an error log tells me that:
>
> MRISreadNewCurvature: incompatible vertex number in file 
> $SUBJECTS_DIR/$sub/surf/lh.curv
>
>
> How do I edit, update or create a curv file to play with the new 
> surface file, or what can I do to get sensical surface coordinates 
> from this data?
>
> Thanks,
> Joel
>
>
>
>
>
>
>
>
> 
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Greve, Douglas N.,Ph.D.]

Hmm, not sure what to tell you. The label is derived directly from the 
annot. If you click on a vertex in the branch, does it appear to be in 
the label based on what displays in the control panel? If you load it on 
the inflated surface, do you still see the branch?

On 10/15/2018 08:42 PM, Ting Li wrote:
>  External Email - Use Caution
>
> The annot file loaded successfully and without any branches. Thanks a lot.
>
> Ting
>> On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. 
>>  wrote:
>>
>> Click on the surface file name in the upper left corner of FreeView,
>> then load the Annotation from the panel just below it. It does not make
>> sense that you would see the branches on the folded surface but not on
>> the inflated.
>>
>> On 10/15/2018 03:06 PM, Ting Li wrote:
>>>  External Email - Use Caution
>>>
>>> I didn't load the annot file. I just use the annot file to create the
>>> label. if I check the clusters in a inflated brain, they are looks
>>> fine. If I need to load annot file for checking, how can I do it?
>>> Thanks a lot.
>>>
>>> Ting
>>>
>>> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>
>>> does the same thing happen when you load the annot file?
>>>
>>> On 10/13/18 10:03 PM, Ting Li wrote:
>>>> External Email - Use Caution
>>>>
>>>> Dear Dr. Douglas,
>>>>
>>>> I can load the label, but some clusters have branches. Some of
>>>> them are just looks fine. Do you know the reason? Thanks a lot.
>>>>
>>>> Regards,
>>>> Ting
>>>>
>>>>
>>>>
>>>>
>>>>> On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
>>>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>>
>>>>> yes, that is fine
>>>>>
>>>>> On 10/11/18 11:21 PM, Ting Li wrote:
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> Dear Dr. Douglas,
>>>>>>
>>>>>> Thank you so much for your response. With your instruction, it
>>>>>> works. This is how I did.
>>>>>>
>>>>>> First, copy the significant cluster annot file from the
>>>>>> simulation fold to one of subject label folder.
>>>>>> Secondly, use the mir_annotation2label command to make this
>>>>>> cluster into a label file
>>>>>> Thirdly, copy this label file to fsaverage label folder
>>>>>> Finally, I can load the label to the fsaverage surf.
>>>>>>
>>>>>> Is this the right procedure? Thanks a lot!
>>>>>>
>>>>>> Regards,
>>>>>> Ting
>>>>>>> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
>>>>>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>>>>>
>>>>>>> Which subject did you load it on? It must be fsaverage. Can
>>>>>>> you send the
>>>>>>> terminal output and command line?
>>>>>>>
>>>>>>> On 10/03/2018 11:31 PM, Ting Li wrote:
>>>>>>>> External Email - Use Caution
>>>>>>>>
>>>>>>>> Dear Freesurfer Expert,
>>>>>>>>
>>>>>>>> I have figured out the problem is that I didn’t specify lh
>>>>>>>> before the
>>>>>>>> annot file. However, in this method, I didn’t get the right
>>>>>>>> label for
>>>>>>>> I have loaded the label into the subject file. It is the
>>>>>>>> scatter points.
>>>>>>>>
>>>>>>>> I want to create label through mri_glm-fit-sim clusters. What
>>>>>>>> command
>>>>>>>> I should use? Please specify it for me. Thanks a lot!
>>>>>>>>
>>>>>>>> Your help means a lot.
>>>>>>>>
>>>>>>>> Regards,
>>>>>>>> Ting
>>>>>>>>> On Oct 3, 2018, at 9:38 PM, Ting Li >>>>>>

Re: [Freesurfer] qdec analysis with more than 2 covariates

[Greve, Douglas N.,Ph.D.]

That looks like the terminal output for qdec. You cannot use qdec with 
your design. If you have questions about the FSGD, I'll be happy to 
answer them.

On 10/16/2018 11:00 AM, vittal korann wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> Thank you for your response.
> I tried the link which you sent yesterday. But got stuck while 
> creating qdec.fsgd file.
> Below i have pasted the terminal output after loading the data.
>
> 1  Left-Lateral-Ventricle  continuous 0
> 2  Left-Inf-Lat-Vent  continuous 0
> 3  Left-Cerebellum-White-Matter  continuous 0
> 4  Left-Cerebellum-Cortex  continuous 0
> 5  Left-Thalamus-Proper  continuous 0
> 6  Left-Caudate  continuous 0
> 7  Left-Putamen  continuous 0
> 8  Left-Pallidum  continuous 0
> 9  3rd-Ventricle  continuous 0
> 10  4th-Ventricle  continuous 0
> 11  Brain-Stem  continuous 0
> 12  Left-Hippocampus  continuous 0
> 13  Left-Amygdala  continuous 0
> 14  CSF  continuous 0
> 15  Left-Accumbens-area  continuous 0
> 16  Left-VentralDC  continuous 0
> 17  Left-vessel  continuous 0
> 18  Left-choroid-plexus  continuous 0
> 19  Right-Lateral-Ventricle  continuous 0
> 20  Right-Inf-Lat-Vent  continuous 0
> 21  Right-Cerebellum-White-Matter continuous 0
> 22  Right-Cerebellum-Cortex  continuous 0
> 23  Right-Thalamus-Proper  continuous 0
> 24  Right-Caudate  continuous 0
> 25  Right-Putamen  continuous 0
> 26  Right-Pallidum  continuous 0
> 27  Right-Hippocampus  continuous 0
> 28  Right-Amygdala  continuous 0
> 29  Right-Accumbens-area  continuous 0
> 30  Right-VentralDC  continuous 0
> 31  Right-vessel  continuous 0
> 32  Right-choroid-plexus  continuous 0
> 33  WM-hypointensities  continuous 0
> 34  Optic-Chiasm  continuous 0
> 35  CC_Posterior  continuous 0
> 36  CC_Mid_Posterior  continuous 0
> 37  CC_Central  continuous 0
> 38  CC_Mid_Anterior  continuous 0
> 39  CC_Anterior  continuous 0
> 40  diagnosis  discrete 2
>     1  Schizophrenia
>     2  Control
> 41  Age  continuous 0
> 42  Birthplace  discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
> 43  Upbringingplace discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
> 44  Livingplace  discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
>                 Continuous Factors:  Mean:       StdDev:
>                 ---  -       ---
>              Left-Lateral-Ventricle 6784.459      3582.583
>                   Left-Inf-Lat-Vent  363.189       163.344
>        Left-Cerebellum-White-Matter  13393.085      2875.553
>              Left-Cerebellum-Cortex  50654.337      7634.479
>                Left-Thalamus-Proper 7044.259      1254.886
>                        Left-Caudate 3267.819       728.738
>                        Left-Putamen 5221.959       863.333
>                       Left-Pallidum 1961.781       357.087
>                       3rd-Ventricle 1068.711       447.579
>                       4th-Ventricle 1673.963       641.339
>                          Brain-Stem  18975.526      3907.934
>                    Left-Hippocampus 3852.407       684.810
>                       Left-Amygdala 1625.463       378.770
>                                 CSF  983.626       305.507
>                 Left-Accumbens-area  587.848       155.803
>                      Left-VentralDC 3977.841       673.114
>                         Left-vessel 28.378        21.035
>                 Left-choroid-plexus  558.441       330.333
>             Right-Lateral-Ventricle 6224.989      3745.143
>                  Right-Inf-Lat-Vent  440.070       168.625
>       Right-Cerebellum-White-Matter  13111.263      2744.138
>             Right-Cerebellum-Cortex  52495.385      7167.728
>               Right-Thalamus-Proper 6732.170      1748.668
>                       Right-Caudate 3305.363       949.074
>                       Right-Putamen 4908.819      1155.840
>                      Right-Pallidum 1774.204       489.167
>                   Right-Hippocampus 3766.470      1019.353
>                      Right-Amygdala 1686.874       437.019
>                Right-Accumbens-area  539.763       151.780
>                     Right-VentralDC 3818.130       666.970
>                        Right-vessel 23.344        16.649
>                Right-choroid-plexus  620.948       414.269
>                  WM-hypointensities 4434.148     10311.009
>                        Optic-Chiasm  198.937        65.369
>                        CC_Posterior  973.467       157.378
>                    CC_Mid_Posterior  637.400       597.617
>                          CC_Central  625.374       497.642
>                     CC_Mid_Anterior  681.052       419.940
>                         CC_Anterior  870.274       237.412
>                                 Age 31.963         7.019
>
> Number of subjects:   27
> Number of factors:    44 (4 discrete, 40 continuous)
> Number of classes:    54
> Number of regressors: 2214
> 
> Data table loading

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

[Greve, Douglas N.,Ph.D.]

which coords are you looking at? They should be the "surface RAS" coords.

On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I couldn't remember if it's 1+ or 1-.  Either way, either direction 
> give similar coordinates that don't match up to what I can see in 
> FreeView.
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Tuesday, October 16, 2018 1:48:14 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [External] Re: [Freesurfer] Nonsensical Vertex Coordinates, 
> please help with interpretation
> When you look at the vertex in matlab, are you correctly accounting for
> the fact that FreeView uses 0-based indexing and matlab uses 1-based?
> Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be
> using 234740 in matlab below
>
> On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
> >
> > External Email - Use Caution
> >
> > I'm trying to make a surface file from a subject's head and to map
> > coordinates to that surface.  If I run:
> >
> >
> > mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol
> > $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2
> > 20 --nhitsmin 2
> >
> > mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255
> > $SUBJECTS_DIR/$sub/surf/lh.seghead
> >
> > and then load lh.seghead in FreeView, it looks as I would expect.
> > Clicking anywhere near a vertex gives the typical output, showing the
> > closest vertex.  All fine and well. However, if I load the file in 
> Matlab:
> >
> >
> > vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
> >
> >
> > my values are nothing near what I'm seeing in Freeview.  For example,
> > FreeView reports:
> >
> >
> > vertex 234741 [-78.50,14.50,26.50]
> >
> >
> > read_surf reports:
> >
> >
> > vertex 234740 0168.98000
> >
> > Of note, an error log tells me that:
> >
> > MRISreadNewCurvature: incompatible vertex number in file
> > $SUBJECTS_DIR/$sub/surf/lh.curv
> >
> >
> > How do I edit, update or create a curv file to play with the new
> > surface file, or what can I do to get sensical surface coordinates
> > from this data?
> >
> > Thanks,
> > Joel
> >
> >
> >
> >
> >
> >
> >
> >
> > 
> > Notice: This UI Health Care e-mail (including attachments) is covered
> > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and
> > is intended only for the use of the individual or entity to which it
> > is addressed, and may contain information that is privileged,
> > confidential, and exempt from disclosure under applicable law. If you
> > are not the intended recipient, any dissemination, distribution or
> > copying of this communication is strictly prohibited. If you have
> > received this communication in error, please notify the sender
> > immediately and delete or destroy all copies of the original message
> > and attachments thereto. Email sent to or from UI Health Care may be
> > retained as required by law or regulation. Thank you.
> > 
> >
> >
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>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered 
> by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and 
> is intended only for the use of the individual or entity to which it 
> is addressed, and may contain information that is privileged, 
> confidential, and exempt from disclosure under applicable law. If you 
> are not the intended recipient, any dissemination, distribution or 
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> received this communication in error, please notify the sender 
> immediately and delete or destroy all copies of the original message 
> and attachments thereto. Email sent to or from UI Health Care may be 
> retained as required by law or regulation. Thank you.
> 
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Re: [Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

[Greve, Douglas N.,Ph.D.]

You can load them in freeview through tksurferfv, something like
tksurferfv fsaverage lh inflated -aparc -ov 
fmcpr.odd.sm5.fsaverage.lh.nii.gz
There's not much to see:)



On 10/16/2018 03:00 PM, Jacob Matthews wrote:
>
> External Email - Use Caution
>
> Hi FS Team,
>
> We are running our first fsfast pipeline, and starting with a single 
> subject to test everything. We successfully ran preproc-sess with the 
> following command:
>
> preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run -sliceorder odd -fsd bold
>
> We wanted to check the outputs. It was clear how to view most 
> intermediate outputs, but we didn't know how to view the surface space 
> outputs:
> fmcpr.odd.sm5.fsaverage.rh.nii.gz
> fmcpr.odd.sm5.fsaverage.lh.nii.gz
>
> Loading them into freeview as surfaces fails. We thought perhaps they 
> needed to be loaded on top of an fsaverage surface, but didn't know 
> where to start this process.
>
> Thanks,
>
> Jacob Matthews
> MRI Specialist
> Rotman Research Institute
> Baycrest Hospital
> 416-785-2500 ext. 3322
>
>
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Re: [Freesurfer] Raw Data for Clusters

[Greve, Douglas N.,Ph.D.]

try
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf 
mc-z.abs.th13.cluster.ocn.dat --excludeid 0


On 10/17/2018 12:57 AM, WON JONG CHWA wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer Experts,
> I am running Qdec 1.4 and I want to extract raw data (in this case, 
> volume) from the significant clusters after Monte-Carlo simulation. In 
> this particular case, the summary file shows 5 significant clusters 
> after correction:
>
> # Cluster Growing Summary (mri_surfcluster)
> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
> # CreationTime 2018/10/16-23:28:21-GMT
> # cmdline mri_surfcluster --in 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh
>  
> --csd 
> /Users/user/MyInstall/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm18/abs/th13/mc-z.csd
>  
> --mask 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/mask.mgh 
> --cwsig 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.mgh
>  
> --vwsig 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.vertex.mgh
>  
> --sum 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.summary
>  
> --ocn 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.mgh
>  
> --oannot 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.annot
>  
> --csdpdf 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.pdf.dat
>  
> --annot aparc --cwpvalthresh 0.05 --o 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.masked.mgh
>  
> --surf white
> # cwd /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only
> # sysname  Darwin
> # hostname N-Volunteer-iMac.local
> # machine  x86_64
> # FixVertexAreaFlag 1
> # FixSurfClusterArea 1
> #
> # Input 
> /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh
> # Frame Number  0
> # srcsubj fsaverage
> # hemi rh
> # surface white
> # annot aparc
> # SUBJECTS_DIR /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only
> # SearchSpace_mm2 64328
> # SearchSpace_vtx 149926
> # Bonferroni 0
> # Minimum Threshold 1.3
> # Maximum Threshold infinity
> # Threshold Sign    abs
> # AdjustThreshWhenOneTail 1
> # CW PValue Threshold: 0.05
> # Area Threshold    0 mm^2
> # CSD thresh  1.30
> # CSD nreps    1
> # CSD simtype  null-z
> # CSD contrast NA
> # CSD confint  90.00
> # Overall max 2.06685 at vertex 34785
> # Overall min -4.82491 at vertex 356
> # NClusters  5
> # Total Cortical Surface Area 64328 (mm^2)
> # FixMNI = 1
> #
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY TalZ    CWP    
> CWPLow    CWPHi   NVtxs   Annot
>    1   -4.825 356   2272.51 60.8   -9.4   -1.7 0.00010  
> 0.0  0.00020  3745  superiortemporal
>    2   -4.419  146292   2658.98 19.8   52.0   -5.7 0.00010  
> 0.0  0.00020  3104  rostralmiddlefrontal
>    3   -4.267  138330   1525.99 35.6   35.2    7.0 0.00460  
> 0.00370  0.00550  1936  rostralmiddlefrontal
>    4   -3.304  140353   1712.65 34.9  -30.2   56.6 0.00220  
> 0.00160  0.00280  3540  postcentral
>    5   -3.050   28351   1096.87 19.6  -34.8   -8.7 0.04530  
> 0.04260  0.04800  1687  parahippocampal
>
> --
> However, when I run the command to extract the raw data from these 
> clusters using this line:
> mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf 
> mc-z.abs.th13.cluster.ocn.dat --excludeid 0
>
> The terminal window outputs this:
>
> rh-Diff-SZ-HC-Intercept-volume user$ mri_segstats --i y.mgh --seg 
> mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat 
> --excludeid 0
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>
> cwd
>
> cmdline mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh 
> --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0
>
> sysnameDarwin
>
> hostname N-Volunteer-iMac.local
>
> machinex86_64
>
> useruser
>
> UseRobust0
>
> Loading mc-z.abs.th13.sig.cluster.mgh
>
> Loading y.mgh
>
> Voxel Volume is 1 mm^3
>
> Generating list of segmentation ids
>
> Found4 segmentations
>
> Computing statistics for each segmentation
>
> 0-468496849.000
>
> 1-254765476.000
>
> 2-116871687.000
>
> Reporting on3 segmentations
>
> Computing spatial average of each frame
>
> 012
>
> Writing to mc-z.abs.th13.cluster.ocn.dat
>
> mri_segstats done
>
> -
>
> So I get a .dat file that only has 3 columns, which does not match up 
> to the 5 that I originally observed after the correction. If you could 
> let me know what the problem is that would be greatly app

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

[Greve, Douglas N.,Ph.D.]

You cannot use QDEC for this. You must use the "command line" stream, 
ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, 
then mri_glmfit-sim. See the tutorial on the wiki.

On 10/17/2018 01:30 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I would like to know how I can run statistical analysis in QDEC on a 
> data set where there are 3 fixed factors each with 2 contrast levels. 
> (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs 
> disease )
>
> Any help would be much appreciated.
> Thank You,
>
>
> -- 
> Azeezat Azeez
> PhD Student
> Department of Biomedical Engineering || New Jersey Institute of 
> Technology
> Graduate School of Biomedical Sciences || Rutgers University
> E: ak...@njit.edu 
>
>
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Re: [Freesurfer] resampling data onto cortical surface

[Greve, Douglas N.,Ph.D.]

Use --s subject instead of --reg (run mri_vol2vol with --help to get 
more info).
btw, if you have multi echo data, you are probably measuring R2*, not R1.

On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
>
> I have R1 values that I want to resample onto the cortical surface. 
> The R1 values were computed from a multi echo
>
> T1 sequence that was also used to create the T1 weighted image that 
> was used in recon-all to produce the cortical surface reconstructions
>
> and thus is inherently in registration to the 001.mgz that was used to 
> start recon. There will be a difference in orientation in the volume
>
> in that orig.mgz is in coronal and in the .mgz format.
>
>
> I was thinking that if I run the first step of recon-all it should 
> give me an volume named orig.mgz that is in registration to the 
> freesurfer space
>
> for the subject ... or else some call to mri_convert reslice_as or 
> whatever is used in the recon-all script to convert 001.mgz to orig.mgz
>
>
>
>
> then my problem is to get a file with the resampling of the R1 onto 
> the cortical surface withR1 values at each vertex.
>
>
> when i work with fmri data I run bbregister and get the transformation 
> from the epi volume to the freesurfer space and then use
>
> mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface
>  --reg bb.register.dat \
>  --projfrac 0.5 --interp nearest \
>  --hemi lh --o lh.sig.mgh
>
> to resample the epi data onto the cortical surface. however in this case the 
> R1 data
> is already in perfect registration to the T1 other than the reorientation and 
> reslicing
> done to prepare the orig.mgz volume.
>
> so can someone tell me what is the proper way to cook this goose
>
> Greg
>
>
>
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Re: [Freesurfer] Surface-based analysis of tfMRI

[Greve, Douglas N.,Ph.D.]

If you do all the preprocessing yourself, then store the output in the 
run folder with a certain name, fmri-denoised.nii.gz, then when you run 
mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.

On 10/22/2018 04:08 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I am trying surface-based analysis of task-fMRI with FS-FAST. However, 
> I would like to apply ICA-based denoising and wavelet-despiking which 
> can be not done with the 'preproc-sess'. I wonder if I can do the 
> preprocessing with other tools before registration with FS anatomical 
> and normalization? If it is available, how can I do it with command line?
>
> Another question is if can I use other template for parcellation 
> during using 'recon-all', such as the template of Human Connectome 
> Project?
>
> Looking forward to your kind reply.
>
> Thank you and best wishes,
>
> Zhi
>
>
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Re: [Freesurfer] resampling data onto cortical surface

[Greve, Douglas N.,Ph.D.]

I would just do
mri_vol2vol --i vin.nii --regheader --targ orig.mgz --o vout.mgz


On 10/22/2018 05:52 PM, GREGORY R KIRK wrote:
>
> External Email - Use Caution
>
> thanks Doug, one more thing to make sure I get it correct.
>
>
> If I have a volume of quantitative MR volumes in the native space of 
> the T1 and I want them to be in registration with the freesurfer space
>
> of this subject I woiuld
>
>
> mri_convert -it nii -ot mgz vin.nii vout.mgz and then
>
> mri_convert vout.mgz vc.mgz --conform --no_scale --nochange
>
>
> so that it is in the freesurfer space but not scaled and not changed 
> from float to uchar, correct ?
>
>
> thanks
>
>
> greg
>
> --------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Monday, October 22, 2018 11:58:51 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] resampling data onto cortical surface
> Use --s subject instead of --reg (run mri_vol2vol with --help to get
> more info).
> btw, if you have multi echo data, you are probably measuring R2*, not R1.
>
> On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
> >
> > External Email - Use Caution
> >
> >
> > I have R1 values that I want to resample onto the cortical surface.
> > The R1 values were computed from a multi echo
> >
> > T1 sequence that was also used to create the T1 weighted image that
> > was used in recon-all to produce the cortical surface reconstructions
> >
> > and thus is inherently in registration to the 001.mgz that was used to
> > start recon. There will be a difference in orientation in the volume
> >
> > in that orig.mgz is in coronal and in the .mgz format.
> >
> >
> > I was thinking that if I run the first step of recon-all it should
> > give me an volume named orig.mgz that is in registration to the
> > freesurfer space
> >
> > for the subject ... or else some call to mri_convert reslice_as or
> > whatever is used in the recon-all script to convert 001.mgz to orig.mgz
> >
> >
> >
> >
> > then my problem is to get a file with the resampling of the R1 onto
> > the cortical surface withR1 values at each vertex.
> >
> >
> > when i work with fmri data I run bbregister and get the transformation
> > from the epi volume to the freesurfer space and then use
> >
> > mri_vol2surf --mov sig.nii \to resample the data onto the cortical 
> surface
> >  --reg bb.register.dat \
> >  --projfrac 0.5 --interp nearest \
> >  --hemi lh --o lh.sig.mgh
> >
> > to resample the epi data onto the cortical surface. however in this 
> case the R1 data
> > is already in perfect registration to the T1 other than the 
> reorientation and reslicing
> > done to prepare the orig.mgz volume.
> >
> > so can someone tell me what is the proper way to cook this goose
> >
> > Greg
> >
> >
> >
> > ___
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>
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Re: [Freesurfer] Surface-based analysis of tfMRI

[Greve, Douglas N.,Ph.D.]

Actually, if you just store the denoised data as f.nii.gz, then run 
preproc-sess it should do ok. It will do motion correction, but it should not 
really do any thing if MC is already done. Just make sure that the image has a 
proper baseline so that the registration will work.

On 10/22/18 11:14 PM, Zhi Li wrote:

External Email - Use Caution

Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I 
register and normalize it to the surface-based space, as 'preproc-sess' do that 
will generate the bilateral cortex in surface and subcortical area in volume?

On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
If you do all the preprocessing yourself, then store the output in the
run folder with a certain name, fmri-denoised.nii.gz, then when you run
mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.

On 10/22/2018 04:08 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I am trying surface-based analysis of task-fMRI with FS-FAST. However,
> I would like to apply ICA-based denoising and wavelet-despiking which
> can be not done with the 'preproc-sess'. I wonder if I can do the
> preprocessing with other tools before registration with FS anatomical
> and normalization? If it is available, how can I do it with command line?
>
> Another question is if can I use other template for parcellation
> during using 'recon-all', such as the template of Human Connectome
> Project?
>
> Looking forward to your kind reply.
>
> Thank you and best wishes,
>
> Zhi
>
>
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Re: [Freesurfer] Surface-based analysis of tfMRI

[Greve, Douglas N.,Ph.D.]

Yes. When you run mkanalysis-sess, you may still have to use the -funcstem

On 10/23/18 10:06 AM, Zhi Li wrote:

External Email - Use Caution

I see. Can I add the flag -nomc to skip motion correction? If I have done the 
slice timing, realignment and denoising, can I use the following command to do 
registration, normalization and smoothing?

preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 
-fwhm 5 -per-run

If I have modified the functional data before I run preproc-sess, will it 
influence the registration and normalization?

On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Actually, if you just store the denoised data as f.nii.gz, then run 
preproc-sess it should do ok. It will do motion correction, but it should not 
really do any thing if MC is already done. Just make sure that the image has a 
proper baseline so that the registration will work.

On 10/22/18 11:14 PM, Zhi Li wrote:

External Email - Use Caution

Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I 
register and normalize it to the surface-based space, as 'preproc-sess' do that 
will generate the bilateral cortex in surface and subcortical area in volume?

On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
If you do all the preprocessing yourself, then store the output in the
run folder with a certain name, fmri-denoised.nii.gz, then when you run
mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.

On 10/22/2018 04:08 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I am trying surface-based analysis of task-fMRI with FS-FAST. However,
> I would like to apply ICA-based denoising and wavelet-despiking which
> can be not done with the 'preproc-sess'. I wonder if I can do the
> preprocessing with other tools before registration with FS anatomical
> and normalization? If it is available, how can I do it with command line?
>
> Another question is if can I use other template for parcellation
> during using 'recon-all', such as the template of Human Connectome
> Project?
>
> Looking forward to your kind reply.
>
> Thank you and best wishes,
>
> Zhi
>
>
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Re: [Freesurfer] FreeSurfer error at selxavg3-sess

[Greve, Douglas N.,Ph.D.]

Not sure what the problem is. The "unrecognized" warning is not a problem. What 
is your mkanalysis-sess command line? What version of FS are you running? You 
can try just deleting the LH and re-running mkanalysis and selxavg

On 10/20/18 12:33 PM, elahe' yargholi wrote:

External Email - Use Caution

Dear FreeSurfer developers,


I have an fMRI data and using the command “selxavg3-sess -s ./SM/Analysis_3_12 
-analysis BioMot_Block_RL_self0m.rh -run-wise -no-con-ok”, analysis of right 
hemisphere is finished correctly.

While for the analysis of left hemisphere as I run “selxavg3-sess -s 
./SM/Analysis_3_12 -analysis BioMot_Block_RL_self0m.lh -run-wise -no-con-ok”, I 
receive the following error:

…

$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /Users/elaheyargholi/Documents/Action_Project/July_2018/SM
Extension format = nii.gz
INFO: key nSliceGroups unrecognized, line 12, skipping
 1 Colors_RGB.mat
Reference to non-existent field 'RmPreStim'.

Error in fast_ldanaflac (line 518)
flac.con(nthcon).rmprestim = cspec.RmPreStim; % 4/8/09

Error in fast_selxavg3b (line 107)
  flac0 = fast_ldanaflac(analysis);



>> --
ERROR: fast_selxavg3() failed\n

It should be mentioned that flags of mkanalysis-sess have the same values for 
both hemispheres.


I do appreciate your attention.

Best Regards,
Elahe'



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Re: [Freesurfer] errors running mri_glmfit

[Greve, Douglas N.,Ph.D.]

You have no subjects in the DIATD-DEVC-sexM class

On 10/18/18 1:53 PM, Azeez, Azeezat wrote:

External Email - Use Caution

Hello I keep getting the same error and am not sure how to address the issue.
I have attached the design matrix and the FSGD file and contrast file of 
interest

Thanks for the help



ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y STATS/lh.DEV_DIA_SEX.thickness.mgh --fsgd 
STATS/DEV_DIA_SEX.fsgd dods --C STATS/mainDEV.mat --surf fsaverage lh --cortex 
--glmdir STATS/lh.DEV_DIA_SEX.thickness.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above

--
Azeezat Azeez




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Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

[Greve, Douglas N.,Ph.D.]

You can use preproc-sess and specify the --meas flag. Run with --help 
for more info.

On 10/18/18 2:08 PM, ts...@rcmd.org wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I have created a custom measure on the pial surface of a number of subjects, 
> and I would like to map the data to the fsaverage subject. (By custom measure 
> I mean something like 'area' or 'curv', i.e., one scalar value per surface 
> vertex.)
>
> I have already done the same for the white surfaces, and it was pretty 
> straight-forward:
> 1) Save the per-vertex data in a curv-format file in 
> SUBJECTS_DIR//surf/?h.
> 2) Run 'recon-all -s  -qcache -measure '
>
> This will map the data to fsaverage and create files named 
> ?h..fwhm.fsaverage.mgh in the surf/ directories as expected 
> (where  is 0, 5, .., 25).
>
> My question is: how can I do the same for my data from the pial surface? Are 
> there any command line options for 'recon-all' (or maybe for mris_preproc) 
> that can do this?
>
> I already tried to put the pial per-vertex data into files named 
> SUBJECTS_DIR//surf/?h.pial., but they are not handled by 
> the recon-all command listed above: no fsaverage files show up for them.
>
> Thanks in advance,
>
> Tim
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
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Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

[Greve, Douglas N.,Ph.D.]

They are the same thing underneath.

On 10/18/18 11:12 AM, Azeez, Azeezat wrote:

External Email - Use Caution

Thank you for the response.
Which smoothing option would you recommend, there is one in mris_preproc, but 
there is also mris_smooth.
Thanks You

On Wed, Oct 17, 2018 at 1:56 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You cannot use QDEC for this. You must use the "command line" stream,
ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit,
then mri_glmfit-sim. See the tutorial on the wiki.

On 10/17/2018 01:30 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I would like to know how I can run statistical analysis in QDEC on a
> data set where there are 3 fixed factors each with 2 contrast levels.
> (DEVELOPMENT : old vs young, SEX: male vs female, DIAGNOSE: Control Vs
> disease )
>
> Any help would be much appreciated.
> Thank You,
>
>
> --
> Azeezat Azeez
> PhD Student
> Department of Biomedical Engineering || New Jersey Institute of
> Technology
> Graduate School of Biomedical Sciences || Rutgers University
> E: ak...@njit.edu<mailto:ak...@njit.edu> 
> <mailto:ak...@njit.edu<mailto:ak...@njit.edu>>
>
>
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--
Azeezat Azeez
PhD Student
Department of Biomedical Engineering || New Jersey Institute of Technology
Graduate School of Biomedical Sciences || Rutgers University
E: ak...@njit.edu<mailto:ak...@njit.edu>



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Re: [Freesurfer] Physiological Noise Regression from rsMRI

[Greve, Douglas N.,Ph.D.]

You will just need to create a text file with one or more columns, one for each 
regressor put this in the run folder (same folder where the raw data are). When 
you run mkanalysis-sess, add
-nuisreg filename N
where N is the number of columns you want to include

On 10/18/18 10:34 AM, Meisler, Steven Lee wrote:

Hi all,


I am currently developing a pipeline to remove physiological noise (respiratory 
and cardiac) from rsMRI images. I am at the point where I have created the 
regressors using fast_retroicor.m from the physiological data logs. When I add 
the columns of the regressors up and plot the result, it appears to create 
pulses at the times when the physiological data peaked. I was wondering if 
anyone knows how to incorporate the regressor files into FreeSurfer. Please let 
me know at your earliest convenience.


Thank you,

Steven


--

Steven L. Meisler, M.S.E.

Clinical Research Coordinator II

Laboratory for NeuroImaging of Coma and 
Consciousness

175 Cambridge Street, Suite 300

Boston, MA 02114

smeis...@mgh.harvard.edu | (617)-726-1884

https://www.linkedin.com/in/steven-meisler

[cid:part4.3C14935A.B4318E6F@mgh.harvard.edu]



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Re: [Freesurfer] Running DICOMS versus FreeSurfer5.3 Output

[Greve, Douglas N.,Ph.D.]

If you have edits you want to save, then you can re-run over 5.3. It should 
work regardless, but it will be a little cleaner if you start from scratch.

On 10/18/18 4:34 AM, Scheffler, F, Mev 
[fre...@sun.ac.za] wrote:

External Email - Use Caution
Dear FreeSurfer Developers

If we want to rerun FreeSurfer dev 6.1 on an old dataset, is it better to rerun 
with the original DICOMS or to rerun over the 5.3 output? Would that even work?

Thanks very much.

Kind regards,

FREDA SCHEFFLER

Research Assistant / PhD Candidate


[email.jpg]


MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika

Tel:  +27 21 938 9771
Email | E-pos:  fre...@sun.ac.za



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Re: [Freesurfer] Surface-based analysis of tfMRI

[Greve, Douglas N.,Ph.D.]

You specify the input you want selxavg3-sess to use. Otherwise, it will try to 
look for things that have been preprocessed.

On 10/23/18 12:17 PM, Zhi Li wrote:

External Email - Use Caution

Thank you. May I ask what do we use the flag -funcstem for? I found that there 
are similar flags in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of 
FreeSufer and not clear about some terms such as 'stem' in both preproc-sess 
and mkanalysis-sess.

On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Yes. When you run mkanalysis-sess, you may still have to use the -funcstem

On 10/23/18 10:06 AM, Zhi Li wrote:

External Email - Use Caution

I see. Can I add the flag -nomc to skip motion correction? If I have done the 
slice timing, realignment and denoising, can I use the following command to do 
registration, normalization and smoothing?

preproc-sess -s sess01 -fsd bold -nomc -nostc -surface fsaverage lhrh -mni305 
-fwhm 5 -per-run

If I have modified the functional data before I run preproc-sess, will it 
influence the registration and normalization?

On Tue, 23 Oct 2018 at 00:08, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Actually, if you just store the denoised data as f.nii.gz, then run 
preproc-sess it should do ok. It will do motion correction, but it should not 
really do any thing if MC is already done. Just make sure that the image has a 
proper baseline so that the registration will work.

On 10/22/18 11:14 PM, Zhi Li wrote:

External Email - Use Caution

Thank you. But the fmri-denoised.nii.gz will be a volume-based data, how can I 
register and normalize it to the surface-based space, as 'preproc-sess' do that 
will generate the bilateral cortex in surface and subcortical area in volume?

On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
If you do all the preprocessing yourself, then store the output in the
run folder with a certain name, fmri-denoised.nii.gz, then when you run
mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm.

On 10/22/2018 04:08 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> I am trying surface-based analysis of task-fMRI with FS-FAST. However,
> I would like to apply ICA-based denoising and wavelet-despiking which
> can be not done with the 'preproc-sess'. I wonder if I can do the
> preprocessing with other tools before registration with FS anatomical
> and normalization? If it is available, how can I do it with command line?
>
> Another question is if can I use other template for parcellation
> during using 'recon-all', such as the template of Human Connectome
> Project?
>
> Looking forward to your kind reply.
>
> Thank you and best wishes,
>
> Zhi
>
>
> ___
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Re: [Freesurfer] Physiological Noise Regression from rsMRI

[Greve, Douglas N.,Ph.D.]

Skull stripping? Are you talking about functional or anatomical data? This only 
applies to FSFAST, not recon-all. You'd run the fsfast preprocessing as normal.

On 10/23/18 12:21 PM, Meisler, Steven Lee wrote:

Thank you! At what point in the processing pipeline should this happen? For 
example, should this happen before or after skull-stripping?


Best,

Steven


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, October 23, 2018 12:12:39 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Physiological Noise Regression from rsMRI

You will just need to create a text file with one or more columns, one for each 
regressor put this in the run folder (same folder where the raw data are). When 
you run mkanalysis-sess, add
-nuisreg filename N
where N is the number of columns you want to include

On 10/18/18 10:34 AM, Meisler, Steven Lee wrote:

Hi all,


I am currently developing a pipeline to remove physiological noise (respiratory 
and cardiac) from rsMRI images. I am at the point where I have created the 
regressors using fast_retroicor.m from the physiological data logs. When I add 
the columns of the regressors up and plot the result, it appears to create 
pulses at the times when the physiological data peaked. I was wondering if 
anyone knows how to incorporate the regressor files into FreeSurfer. Please let 
me know at your earliest convenience.


Thank you,

Steven


--

Steven L. Meisler, M.S.E.

Clinical Research Coordinator II

Laboratory for NeuroImaging of Coma and 
Consciousness<https://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605>

175 Cambridge Street, Suite 300

Boston, MA 02114

smeis...@mgh.harvard.edu<mailto:smeis...@mgh.harvard.edu> | (617)-726-1884

https://www.linkedin.com/in/steven-meisler

[cid:part4.F599AACC.96853E0E@mgh.harvard.edu]



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Re: [Freesurfer] Physiological Noise Regression from rsMRI

[Greve, Douglas N.,Ph.D.]

you can give it multiple -nuisreg options, so keep them in separeate files if 
you want

On 10/23/18 12:23 PM, Meisler, Steven Lee wrote:

Also, I currently have one regressor file for cardiac noise and one for 
respiratory, each with multiple columns (each column representing a Fourier 
decomposition term). Should I consolidate these two txt files into one txt 
file, or should I call -nuisreg twice? Thanks again.


Best,

Steven


From: Meisler, Steven Lee
Sent: Tuesday, October 23, 2018 12:21:08 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Physiological Noise Regression from rsMRI


Thank you! At what point in the processing pipeline should this happen? For 
example, should this happen before or after skull-stripping?


Best,

Steven


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Tuesday, October 23, 2018 12:12:39 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Physiological Noise Regression from rsMRI

You will just need to create a text file with one or more columns, one for each 
regressor put this in the run folder (same folder where the raw data are). When 
you run mkanalysis-sess, add
-nuisreg filename N
where N is the number of columns you want to include

On 10/18/18 10:34 AM, Meisler, Steven Lee wrote:

Hi all,


I am currently developing a pipeline to remove physiological noise (respiratory 
and cardiac) from rsMRI images. I am at the point where I have created the 
regressors using fast_retroicor.m from the physiological data logs. When I add 
the columns of the regressors up and plot the result, it appears to create 
pulses at the times when the physiological data peaked. I was wondering if 
anyone knows how to incorporate the regressor files into FreeSurfer. Please let 
me know at your earliest convenience.


Thank you,

Steven


--

Steven L. Meisler, M.S.E.

Clinical Research Coordinator II

Laboratory for NeuroImaging of Coma and 
Consciousness<https://www.massgeneral.org/neurology/research/researchlab.aspx?id=1605>

175 Cambridge Street, Suite 300

Boston, MA 02114

smeis...@mgh.harvard.edu<mailto:smeis...@mgh.harvard.edu> | (617)-726-1884

https://www.linkedin.com/in/steven-meisler

[cid:part4.B03DADC2.C3689E71@mgh.harvard.edu]



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Re: [Freesurfer] Myelinated cortical thickness ratio map

[Greve, Douglas N.,Ph.D.]

You can use the per-voxel regressor (--pvr) option to mri_glmfit. Search 
through the mail archives for how to use it

On 10/23/2018 06:34 AM, Damien MARIE wrote:
>
> External Email - Use Caution
>
> Hi Matt,
>
> Many thanks for your prompt reply, you are right.
>
> Any tips on how I could do that?
>
> Should I regress out cortical thickness from my myelin maps at the 
> individual level, save the individual output myelin maps and run 
> analyses on the latter? If yes how?
>
> That’s really important to me otherwise a reviewer could claim the 
> myelin differences we detect might be supported by cortical thickness 
> variations and not myelin…
>
> Thank you and best,
>
> Damien
>
>
>
>> Glasser, Matthew 
>> Mon,
>>  
>> 22 Oct 2018 12:57:43 -0700 
>> 
>>
>> Regression would be better than division.
>> Matt.
>>
>> From:
>> > >
>>   on behalf of Damien MARIE http://damien.ma/>...@unige.ch 
>> >
>> Reply-To: Freesurfer support list
>> > >
>> Date: Monday, October 22, 2018 at 8:54 AM
>> To: "freesurfer@nmr.mgh.harvard.edu 
>> "
>>  
>> > >
>> Subject: [Freesurfer] Myelinated cortical thickness ratio map
>>
>>
>>  External Email - Use Caution
>>
>> Dear experts,
>>
>> I am working with R1 maps that I project on the surface. The goal is to look 
>> at
>> intra-cortical myelin.
>>
>> I detect interesting effects between two groups. Now I would like to compute
>> myelinated cortical thickness ratio maps, in order to control for the effect 
>> of
>> cortical thickness variations occurring with gyrification.
>>
>> Here is a paper where they describe a way to compute those myelinated 
>> cortical
>> thickness ratio map with MIPAV and the MPI-CBS toolbox :
>> https://www.ncbi.nlm.nih.gov/pubmed/29321232
>> «  The proportional thickness of the myelinated part of the cortex in 
>> relation
>> to its overall thickness (myelinated cortical thickness) was computed with a
>> fuzzy classification technique combining information about radial and
>> tangential fibers.  «
>>
>> 1- Is it possible to do the same in FreeSurfer?
>>
>> 2- What about dividing my individual myelin maps by the individual cortical
>> thickness maps? Is it possible to do that in FreeSurfer? SPM ImCalc would do
>> the job in the volume but I don’t know how I could do that in FreeSurfer.
>>
>> Any comments / other suggestions are welcome.
>>
>> Thank you and best,
>>
>> Damien
>>
>
>
>
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Re: [Freesurfer] Paired Analysis Contrasts

[Greve, Douglas N.,Ph.D.]

On 10/24/2018 09:45 PM, srishti goel wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to perform a paired analysis for a data set that has 
> subjects' who belong to either group1 or group2 and have data at time 
> point1 (tp1) and time point2 (tp2). I am following all the steps on 
> the wiki but I want to clarify if the contrasts I plan to use for my 
> analyses are appropriate.
>
> For my analyses, I only have two groups and no covariates. I am 
> interested to know if the decrease in cortical thickness of subjects 
> in group 1 across tp1 and tp2 is more than the decrease in cortical 
> thickness of subjects in group 2 across tp1 and tp2. The contrast I 
> think should be used for this is: 1 -1. Is that correct?
Yes, if you first take the difference between tp1 and tp2.
>
> I am also interested to know if the cortical thickness decreased for 
> subjects regardless of the groups so should I use the contrast: 1 for 
> that?
Assuming you are keeping 2 groups, then use
  0.5 0.5
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu 
> skype: srishti.goel12
>
>
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Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

[Greve, Douglas N.,Ph.D.]

On 10/25/2018 11:31 AM, ts...@rcmd.org wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> thanks for your answer.
>
> Did you by any chance mean mris_preproc instead of preproc-sess? The latter 
> seems to have no --meas flag according to the help (and a quick grep through 
> the script file).
Yes, sorry.
>
> I ended up placing the curv files in /surf/?h..pial and the running:
> recon-all -s $SUBJECT -qcache -no-isrunning -measure ${MEASURE}.pial
>
> This seems to also have done the trick, and it seems to be the way it is done 
> by recon-all for the area.
That should work, but you should have been able to use mris_preproc 
directly (recon-all just calls mris_preproc).
>
> I only expected that you have to explicitly define that the values should be 
> mapped to the pial surface of the fsaverage subject. But if vertex #n in the 
> pial is the closest vertex to vertex #n in the white, maybe no special 
> handling is needed?
Right, the white and the pail use the same registratin
>
> Tim
>
>> On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." 
>>  wrote:
>>
>>
>> You can use preproc-sess and specify the --meas flag. Run with --help
>> for more info.
>>
>> On 10/18/18 2:08 PM, ts...@rcmd.org wrote:
>>>   External Email - Use Caution
>>>
>>> Dear FreeSurfer experts,
>>>
>>> I have created a custom measure on the pial surface of a number of 
>>> subjects, and I would like to map the data to the fsaverage subject. (By 
>>> custom measure I mean something like 'area' or 'curv', i.e., one scalar 
>>> value per surface vertex.)
>>>
>>> I have already done the same for the white surfaces, and it was pretty 
>>> straight-forward:
>>> 1) Save the per-vertex data in a curv-format file in 
>>> SUBJECTS_DIR//surf/?h.
>>> 2) Run 'recon-all -s  -qcache -measure '
>>>
>>> This will map the data to fsaverage and create files named 
>>> ?h..fwhm.fsaverage.mgh in the surf/ directories as expected 
>>> (where  is 0, 5, .., 25).
>>>
>>> My question is: how can I do the same for my data from the pial surface? 
>>> Are there any command line options for 'recon-all' (or maybe for 
>>> mris_preproc) that can do this?
>>>
>>> I already tried to put the pial per-vertex data into files named 
>>> SUBJECTS_DIR//surf/?h.pial., but they are not handled by 
>>> the recon-all command listed above: no fsaverage files show up for them.
>>>
>>> Thanks in advance,
>>>
>>> Tim
>>>
>>> --
>>> Dr. Tim Schäfer
>>> Postdoc Computational Neuroimaging
>>> Department of Child and Adolescent Psychiatry, Psychosomatics and 
>>> Psychotherapy
>>> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>>>
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>>
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> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
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Re: [Freesurfer] First level modelling in task-based fMRI data

[Greve, Douglas N.,Ph.D.]

On 10/26/2018 10:53 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer Experts,
>
> Now I am trying FS-FAST in analyzing task-based fMRI data. We have two 
> runs for each participant. However, there were not enough events in 
> some runs of some participants. Hence we'd like to concatenate the 
> preprocessed images of two runs into one rather than model them 
> separately. How can we combine the preprocessed surface and 
> sub-cortical data of each run into one?
This happens automatically. Just make sure the paradigm files are correct.
>
> In addition. can we use FreeSurfer or FS-FAST to analyse task-based 
> functional connections, such as psychophysiological interactions 
> analysis and dynamic causal modelling? Do you have any suggestions?
Sorry, this is not offered in FSFAST. You can try this toolbox 
https://www.nitrc.org/projects/gppi (I have not used it before, so I 
can't say how well it works).
>
> Thank you and best wishes,
>
> Zhi
>
>
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Re: [Freesurfer] freesurfer selxavg3-sess error

[Greve, Douglas N.,Ph.D.]

When you ran mkanalysis-sess, did you specify two event types? You only 
have one non-null event in your paradigm file.

On 10/28/2018 08:57 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Thanks! Now it's loading correctly my event file.
> However, when I run selxavg3-sess I get this error message:
>
> selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF -no-con-ok
>
> outanadir = 
> /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF/bold/FF-MonkeyCassis.sm03.lh
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> Excluding 2 points
> parfiles condition id list:  1
> ERROR: found 1 non-null conditions, expected 2
> --
> ERROR: fast_selxavg3() failed\n
>
> This is my even file:
>
> 0    1    32    1    ON
> 32    0    32    1    OFF
> 64    1    32    1    ON
> 96    0    32    1    OFF
> 128    1    32    1    ON
> 160    0    32    1    OFF
> 192    1    32    1    ON
> 224    0    32    1    OFF
>
> Thanks for the help!
> Best
> Francesca
>
> Il giorno gio 3 mag 2018 alle ore 00:49 Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>
> oops, sorry. Looks like it is having a problem loading your paradigm
> file. Check that. If the error does not pop out to you then send
> it to me.
>
>
> On 05/02/2018 10:06 AM, Francesca Strappini wrote:
> > Hi, sorry, maybe my last email got lost. Is there anything I can
> try
> > to fix this problem with selxavg3-sess?
> >
> > Thanks!
> > Best
> > Francesca
> >
> > 2018-04-24 20:35 GMT+03:00 Francesca Strappini
> >  
>  >>:
> >
> >     Thank you for the reply!
> >     I deleted the contrasts and run this command line:
> >
> >     selxavg3-sess -a FF-MonkeyCassis.sm03.rh -s MonkeyCassis-FF
> -no-con-ok
> >
> >
> >     --- matlab output 
> >     MATLAB is selecting SOFTWARE OPENGL rendering.
> >
> >     < M A T L A B (R) >
> >       Copyright 1984-2016 The MathWorks, Inc.
> >        R2016b (9.1.0.441655) 64-bit (glnxa64)
> >      September 7, 2016
> >
> >
> >     To get started, type one of these: helpwin, helpdesk, or demo.
> >     For product information, visit www.mathworks.com
> 
> >     .
> >
> >     >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> >     >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> >     >> /usr/local/freesurfer/matlab/MRIread.m
> >     >> >> >> starting fast_selxavg3b
> >
> >
> >     #@# MonkeyCassis-FF ###
> >     /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF
> >     -
> >     $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
> >     -
> >     outtop = /usr/local/freesurfer/fsfast/Monkeys
> >     Extension format = nii.gz
> >     INFO: key nSliceGroups unrecognized, line 11, skipping
> >     Subscripted assignment dimension mismatch.
> >
> >     Error in fast_ldpar4 (line 97)
> >       par4(nthrow,1) = tonset;
> >
> >     Error in flac_customize (line 121)
> >     [par partype] = fast_ldpar4(parpath);
> >
> >     Error in fast_selxavg3b (line 129)
> >     flac0 = flac_customize(flac0);
> >
> >     >> --
> >     ERROR: fast_selxavg3() failed\n
> >
> >
> >     2018-04-24 20:27 GMT+03:00 Douglas Greve
> mailto:dgr...@mgh.harvard.edu>
> >      >>:
> >
> >         Try deleting the contrasts (.mat files) and rerunning
> >
> >
> >         On 4/24/18 5:48 AM, Francesca Strappini wrote:
> >>
> >>
> >>         Dear FreeSurfer experts,
> >>
> >>         I'm trying to analyze some monkey functional data. I
> got this
> >>         error message with selxavg3-sess.
> >>
> >>         I run the following commands:
> >>
> >>         mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast
> >>         ON-vs-OFF -a 1 -c 0
> >>         mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast
> >>         ON-vs-OFF -a 1 -c 0
> >>         preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s
> >>         MonkeyCassis-FF -fsd bold -per-session
> >>         selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF
> >>
> >>
> >>         --- matlab output 

Re: [Freesurfer] aparcstats2table --parcs-from-file trouble

[Greve, Douglas N.,Ph.D.]

If you are using output froom mri_segstats, then you need to use 
asegstats2table, not aparcstats2table. It can be confusing ...

On 11/01/2018 05:06 PM, Figueiro Longo, Maria Gabriela wrote:
>
> Hi,
>
>
> I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg 
> --> mri_segstats .
>
> Now I am trying to extract the summary table using aparcstats2table 
> --parcs-from-file , but every time an error message pops up:
>
>
> ERROR: cannot read 
>
>
> The stats files generated by the mri_segstats look correct (similar 
> with the other files in the directory) and I can read the volumes of 
> each individual.
>
>
> The last command that has an error is:
>
>
> aparcstats2table --qdec-long qdec.txt --hemi lh --meas volume 
> --parcs-from-file  --tablefile volumes.txt
>
>
> I really appreciate any help!
>
> Thanks!
>
> Gabriela
>
>
>
>
>
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Re: [Freesurfer] GLM

[Greve, Douglas N.,Ph.D.]

Use the first one. Not sure what you mean by your multiple comparisons 
question

On 11/01/2018 11:20 PM, 郑凤莲 wrote:
>
> External Email - Use Caution
>
> Hi experts,
>
> I am using FS 6.0 for analyzing the cortical thickness difference 
> between 3 groups: patient1, patient2 and control. In DODS model, I 
> need to creat 2 files, FSDG and mtx file. And we have 3 variables: 
> age, gender and cortical thickness.
> 1. The FSDG file is:
> GroupDescriptorFile 1
> Title Tutorial
> Class patient1-male
> Class patient1-female
> Class patient2-male
> Class patient2-female
> Class control-male
> Class control-female
> Variables                                 age
> Input subject1 patient1-female 20
> Input subject2 patient1-male    33
> Input subject3 patient2-female 40
> Input subject4 patient2-male    50
> Input subject5 control-male    30
> Input subject6 control-female 35
> And there is another way:
> GroupDescriptorFile 1
> Title Tutorial
> Class patient1
> Class patient2
> Class control
> Variables                     sex age
> Input subject1 patient1 1   20
> Input subject2 patient1 2   33
> Input subject3 patient2 1   40
> Input subject4 patient2 2   50
> Input subject5 control   2   30
> Input subject6 control   1   35
> What I want to confirm is that if I want to adjust for sex and age, 
> which one is right?
> Another question is that is there any way to get the multiple 
> comparisons between groups simultaneously?
> I am looking forward to your reply. Thanks very much.
>
> Sincerely,
> Zheng
>
>
>
>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

Are you using FSFAST? If you run the  preprocessing (preproc-sess), then 
it will get you most of the way there.

On 11/05/2018 10:16 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer experts,
>
> May I ask how can I modify the surface-based fMRI data, such as 
> combing two independent sessions into one or dividing one 4D into a 
> series of 3D surface-based fMRI files in which each one denotes a 
> single volume/TR? Thank you very much.
>
> Best wishes,
>
> Zhi
>
>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

If you just want to concatenate you can use something like
mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz 
002/fmcpr.up.sm5.fsaverage.lh.nii.gz 
003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o 
all.fmcpr.up.sm5.fsaverage.lh.nii.gz




On 11/07/2018 12:30 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hi Dougles,
>
> Thank your for your reply. Now I am using FSFAST, but I didn't find 
> flags in prepro-sess which can be used in combing or dividing fMRI 
> data. Using the following code I could get three files for each run 
> (left cortical surface, right cortical surface and sub-cortical volume):
>
> /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface 
> fsaverage lhrh -mni305 -fwhm 5 -per-session/
>
> Can I use preproc-sess to combine files from different runs, and 
> discard the first 4 time points of each run? If so, could you please 
> give me a example?
>
> Thanks and best,
>
> Zhi
>
>
> On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Are you using FSFAST? If you run the  preprocessing
> (preproc-sess), then
> it will get you most of the way there.
>
> On 11/05/2018 10:16 AM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer experts,
> >
> > May I ask how can I modify the surface-based fMRI data, such as
> > combing two independent sessions into one or dividing one 4D into a
> > series of 3D surface-based fMRI files in which each one denotes a
> > single volume/TR? Thank you very much.
> >
> > Best wishes,
> >
> > Zhi
> >
> >
> > ___
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Re: [Freesurfer] GLM

[Greve, Douglas N.,Ph.D.]

Sounds like you need an F-test, eg, create a contrast like
1 1 -1 -1  0  0 0 0 0 0 0 0
1 1  0  0 -1 -1 0 0 0 0 0 0

This tests the null hypothesis that p1==p2==control



On 11/07/2018 10:11 AM, 13181786167 wrote:
>
> External Email - Use Caution
>
> Thanks for your reply. Using the first one, We can obtain the sig.mgh 
> among 3 groups. If I want to obtain the results simultaneously between 
> patient 1 and 2, patient 1 and control, patient 2 and control. What 
> should I do.
>
> Sincerely,
> Zheng
>
>
>
>   
> 郑凤莲
> 邮箱：13181786...@163.com
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?iconUrl=http%3A%2F%2Fmail-online.nosdn.127.net%2F045c9f9c64b625832c45daba6225f5de.jpg&name=%E9%83%91%E5%87%A4%E8%8E%B2&uid=13181786167%40163.com&ftlId=1&items=%5B%22%E9%82%AE%E7%AE%B1%EF%BC%9A13181786167%40163.com%22%5D>
>  
>
>
> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail88> 
> 定制
>
> On 11/07/2018 22:57, Greve, Douglas N.,Ph.D.
> <mailto:dgr...@mgh.harvard.edu> wrote:
> Use the first one. Not sure what you mean by your multiple
> comparisons
> question
>
> On 11/01/2018 11:20 PM, 郑凤莲 wrote:
> >
> > External Email - Use Caution
> >
> > Hi experts,
> >
> > I am using FS 6.0 for analyzing the cortical thickness
> difference
> > between 3 groups: patient1, patient2 and control. In DODS
> model, I
> > need to creat 2 files, FSDG and mtx file. And we have
> 3 variables:
> > age, gender and cortical thickness.
> > 1. The FSDG file is:
> > GroupDescriptorFile 1
> > Title Tutorial
> > Class patient1-male
> > Class patient1-female
> > Class patient2-male
> > Class patient2-female
> > Class control-male
> > Class control-female
> > Variables                                 age
> > Input subject1 patient1-female 20
> > Input subject2 patient1-male    33
> > Input subject3 patient2-female 40
> > Input subject4 patient2-male    50
> > Input subject5 control-male    30
> > Input subject6 control-female 35
> > And there is another way:
> > GroupDescriptorFile 1
> > Title Tutorial
> > Class patient1
> > Class patient2
> > Class control
> > Variables                     sex age
> > Input subject1 patient1 1   20
> > Input subject2 patient1 2   33
> > Input subject3 patient2 1   40
> > Input subject4 patient2 2   50
> > Input subject5 control   2   30
> > Input subject6 control   1   35
> > What I want to confirm is that if I want to adjust for sex
> and age,
> > which one is right?
> > Another question is that is there any way to get the multiple
> > comparisons between groups simultaneously?
> > I am looking forward to your reply. Thanks very much.
> >
> > Sincerely,
> > Zheng
> >
> >
> >
> >
> > ___
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Re: [Freesurfer] MatrixReadTxT: could not scan value [1][1]

[Greve, Douglas N.,Ph.D.]

It is probably trying to use a default bval and bvec file, but it can't 
find it. If you have your bvals and bvects, try passing them explicitly 
to dt_recon

On 11/07/2018 11:56 AM, Anwar Shatil wrote:
>
> External Email - Use Caution
>
> Hello Doug:
>
>
> My dti_recon is getting stuck at the "Fitting Tensor" stage. I was 
> wondering if there is any solution to the problem "MatrixReadTxT: 
> could not scan value [1][1]". My log file is attached here and the 
> problem can be found right at the bottom. Is this a bug? What is the 
> solution?
>
>
> There were similar reports on this earlier but nobody answered.
>
>
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+%5C%5D+dt_recon%22&o=newest&f=1
>
>
> I am using FS 6.0 in MacOS.
>
>
> Best,
>
>
> Anwar
>
>
>
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Re: [Freesurfer] mris_apply_reg failing for area/volume

[Greve, Douglas N.,Ph.D.]

Can you send the terminal output that includes the error?

On 11/06/2018 06:36 PM, James Michael Roe wrote:
>  External Email - Use Caution
>
> Hi Bruce
>
> I realise that my last message made it sound as though the problem was fixed.
> However, I was only confirming that the files load fine in freeview (are not 
> corrupted) as asked.
> The issue of many subs area and volume files failing to register when using 
> --jac is still unsolved
>
> Appreciate the support.
>
> Thanks
>
> James
>
> 
> From: James Michael Roe
> Sent: 31 October 2018 19:45
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> Hi Bruce
>
> Can confirm that both files (rh.area & rh.volume) load fine in freeview
>
> Thanks for the help!
>
> James
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 29 October 2018 15:43
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> Hi James
>
> can you verify that the various files (e.g.
> /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)
>
> are intact by loading them into freeview? For the area file you will of
> course have to load it as an overlay not as a surface (since it isn't a
> surface)
>
> cheers
> Bruce
> On Mon, 29 Oct 2018, James Michael Roe wrote:
>
>>  External Email - Use Caution
>>
>>
>> ​Dear freesurfer experts
>>
>>
>>
>> I’m running the following commands to register RH area and volume files per 
>> sub to both hemispheres
>> of a symmetrical template following Xhemi routines.
>>
>> The commands have already worked for many subs, but are failing to write the 
>> target file for a
>> number of others (and all run fine without the –-jac flag)
>>
>>
>> #right to left
>>
>> mris_apply_reg \
>>
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>
>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>>
>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>>
>> --jac
>>
>>
>>
>> #right to right
>>
>> mris_apply_reg \
>>
>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>
>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>>
>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>>
>> --jac
>>
>>
>>
>>
>> The error is not template-specific as the output is the same using 
>> fsaverage_sym
>>
>> Attached is the log file.
>>
>>
>>
>> Thanks in advance!
>>
>>
>>
>>
>> ​- James
>>
>>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

First run
mri_convert --nskip 4 
fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
then concat the skip files


On 11/07/2018 01:42 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> How can I discard the first 4 time points of each run during 
> concatenating several runs? I know I can skip the first 4 time points 
> with the flag /-nskip 4/ in configuring a analysis, but this condition 
> can be only applicable when each run is modelled into the GLM 
> independently, right? If I feed the /mkanalysis-sess/ with the 
> concatenated file, it will only skip the first 4 time points of the 
> 1st run in this file.
>
> In addition, if my task design is event-related, do I need to set the 
> duration of each stimulus as 0?
>
> Thanks and best
>
> On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>
> If you just want to concatenate you can use something like
> mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> 002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> 003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> all.fmcpr.up.sm5.fsaverage.lh.nii.gz
>
>
>
>
> On 11/07/2018 12:30 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dougles,
> >
> > Thank your for your reply. Now I am using FSFAST, but I didn't find
> > flags in prepro-sess which can be used in combing or dividing fMRI
> > data. Using the following code I could get three files for each run
> > (left cortical surface, right cortical surface and sub-cortical
> volume):
> >
> > /preproc-sess -sf subjects -fsd task_name -sliceorder so -surface
> > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> >
> > Can I use preproc-sess to combine files from different runs, and
> > discard the first 4 time points of each run? If so, could you
> please
> > give me a example?
> >
> > Thanks and best,
> >
> > Zhi
> >
> >
> > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>
> wrote:
> >
> >     Are you using FSFAST? If you run the  preprocessing
> >     (preproc-sess), then
> >     it will get you most of the way there.
> >
> >     On 11/05/2018 10:16 AM, Zhi Li wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Hello FreeSurfer experts,
> >     >
> >     > May I ask how can I modify the surface-based fMRI data,
> such as
> >     > combing two independent sessions into one or dividing one
> 4D into a
> >     > series of 3D surface-based fMRI files in which each one
> denotes a
> >     > single volume/TR? Thank you very much.
> >     >
> >     > Best wishes,
> >     >
> >     > Zhi
> >     >
> >     >
> >     > ___
> >     > Freesurfer mailing list
> >     > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >     <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >     ___
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
>
>
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Re: [Freesurfer] How to combine and divide surface-based fMRI data?

[Greve, Douglas N.,Ph.D.]

are you trying to use FSFAST to do the entire fmri anlaysis? If so, then 
follow the tutorial as it will handle the skipped TRs and the 
concatenation for you. If not, then you don't need a paradigm file

On 11/07/2018 02:14 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Great! So I also need to subtract 8 seconds from the onset time of 
> each stimulus when I make the /paradigm file/, right? If the duration 
> of stimulus is smaller than 1 second, such as 0.05 second, do I need 
> to change its duration to 0 in a event-related deign?
>
>
> On Wed, 7 Nov 2018 at 13:51, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> First run
> mri_convert --nskip 4
> fmcpr.up.sm5.fsaverage.lh.nii.gzfmcpr.up.sm5.fsaverage.lh.skip4.nii.gz
> then concat the skip files
>
>
> On 11/07/2018 01:42 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > How can I discard the first 4 time points of each run during
> > concatenating several runs? I know I can skip the first 4 time
> points
> > with the flag /-nskip 4/ in configuring a analysis, but this
> condition
> > can be only applicable when each run is modelled into the GLM
> > independently, right? If I feed the /mkanalysis-sess/ with the
> > concatenated file, it will only skip the first 4 time points of the
> > 1st run in this file.
> >
> > In addition, if my task design is event-related, do I need to
>     set the
> > duration of each stimulus as 0?
> >
> > Thanks and best
> >
> > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>
> wrote:
> >
> >
> >     If you just want to concatenate you can use something like
> >     mri_concat 001/fmcpr.up.sm5.fsaverage.lh.nii.gz
> >     002/fmcpr.up.sm5.fsaverage.lh.nii.gz
> >     003/fmcpr.up.sm5.fsaverage.lh.nii.gz --o
> >     all.fmcpr.up.sm5.fsaverage.lh.nii.gz
> >
> >
> >
> >
> >     On 11/07/2018 12:30 PM, Zhi Li wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Hi Dougles,
> >     >
> >     > Thank your for your reply. Now I am using FSFAST, but I
> didn't find
> >     > flags in prepro-sess which can be used in combing or
> dividing fMRI
> >     > data. Using the following code I could get three files for
> each run
> >     > (left cortical surface, right cortical surface and
> sub-cortical
> >     volume):
> >     >
> >     > /preproc-sess -sf subjects -fsd task_name -sliceorder so
> -surface
> >     > fsaverage lhrh -mni305 -fwhm 5 -per-session/
> >     >
> >     > Can I use preproc-sess to combine files from different
> runs, and
> >     > discard the first 4 time points of each run? If so, could you
> >     please
> >     > give me a example?
> >     >
> >     > Thanks and best,
> >     >
> >     > Zhi
> >     >
> >     >
> >     > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D.
> >     > mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>
> >     <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>>>>
> >     wrote:
> >     >
> >     >     Are you using FSFAST? If you run the preprocessing
> >     >     (preproc-sess), then
> >     >     it will get you most of the way there.
> >     >
> >     >     On 11/05/2018 10:16 AM, Zhi Li wrote:
> >     >     >
> >     >     > External Email - Use Caution
> >     >     >
> >     >     > Hello FreeSurfer experts,
> >     >     >
> >     >     > May I ask how can I modify the surface-based fMRI data,
> >     such as
> >     >     > combing two independent sessions into one or
> dividing one
> >     4D into a
> >     >     > series of 3D surface-based fMRI files in which each one
> >     denotes a
> >     >   

Re: [Freesurfer] Desikian-Killiany and Destrieux atlas

[Greve, Douglas N.,Ph.D.]

I'm not sure what you mean. The atlas is distributed with FS.

On 11/07/2018 05:09 PM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Hello Freesurfer devs,
>
>
> Is there available any Desikian-Killiany and Destrieux atlas template 
> or image downloadable with all brain labels of the atlas? I would to 
> use this image to show my results in a lab meeting? I would need 
> somethig similar that the lookup table used in the freeview.
>
>
> Cheers,
>
> -- 
> *Miguel Ángel Rivas Fernández*
>
>
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Re: [Freesurfer] T-value in QDEC or FREESURFER

[Greve, Douglas N.,Ph.D.]

On 11/03/2018 02:20 AM, Vikas Bandalli wrote:
>
> External Email - Use Caution
>
> Dear  freesurfer team.
>
> I am running an analysis betweene two groups Normal and Patients.
> Here is an example of my particular design
> diagnosis :- Normal vs Bipolar
> Co-variate :- Age
> Nuisance factor :- Total_Intra cranial volume
>
> I would please like to know a couple of things related to QDEC
> 1.I am looking for difference in volume between patients and controls 
> and the analysis. For correcting for multiple comparisons I ran Monte 
> carlo - Z simulation at threshold of 1.3
> My understanding is the analysis overall runs a two-tailed t-test 
> first and then when we select to run MC-z simulation it iterates for 
> multiple comparisions (by repeating the saem say 1000 times ) and 
> gives out 'clusterwise p-value'
> Is my understanding correct?
It synthesizes a z-field, then smoothes it based on the smoothness of 
the residual of the real data, then thresholds, finds the max cluster 
size. It then repeats 1000 times. It then computes the p-value of your 
cluster based on the number of times it saw a cluster of the same size 
or bigger out of the 1000 trials. Note: for a threshold of 1.3, we 
recommend that you do permutation instead since the cluster p-value is 
very liberal using the MCZ simulation.
>
> 2.I would like to extract T-values for the same . Are we getting 
> cluster wise T-value similar to cluster wise p-value ?
> in the terminal
The cluster pvalue is not based on a t-test. You can get t-value from 
the original voxel-wise analysis. Look in the output folder under each 
contrast. You will find F.mgh and gamma.mgh. t = sign(gamma)*sqrt(F) 
(assuming it is a t-contrast and not an F)
>
> 3. Where would I find t-values for the analysis ???
See above
>
> 4.Are there any methods to extract T-values in qdec or freesurfer . If 
> so,please specify.
>
> I am enclosing screenshots from my analysis for the same . Kindly 
> request you to please have a look please help me out with this ??
>
> Thanking You,
>
> Yours sincerely ,
> Dr.Vikas Bandalli
>
> --
> Bangalore Medical College and Research Institute (BMCRI),
> Bangalore,India,
> Ph : +918904286825


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Re: [Freesurfer] dcmunpack Error

[Greve, Douglas N.,Ph.D.]

You have to specify an output directory with -targ and the runs you want 
to unpack with -run. See the help (ie, run dcmunpack with -help)

On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Developers,
> I was going to reconstruct MPRAGE images from GE 3T machine.
> First I used this command:
> /dcmunpack -src . -scanonly scan.log/
>
> It made just /scan.log/ file for me. Then I used this command:
> /unpacksdcmdir -src / -targ  
> -scanonly scan.log/
>
> However, it made 3 files for me; dicomdir.sumfile, parse.status and 
> unpack.log, but they were 0 bites. Furthermore, the following message 
> also appeared on the terminal:
>
> /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> See logfile /hpc/mtay316/tutorial4/practice_with_data//unpack.log for 
> more details/
>
> I used this command for SIEMENS data and it worked. Apparently this 
> code just works on SIEMENS data not GE. So now what is the code that I 
> can use for GE dcm images?
>
> 1) FREESURFER Version: 
> freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> 2) Platform: Ubuntu 16.04 LTS
> 3) unpack.log : see attached
>
> Regards
>
>
> -- 
> *Maryam Tayebi*
>
> PhD Candidate of Bioengineering
> Auckland Bioengineering Institute, University of Auckland, Auckland, 
> New Zealand
>
>
>
> MSc of Medical Imaging
> University of Manchester, Manchester, UK
>
>
> ___
> Freesurfer mailing list
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Re: [Freesurfer] dcmunpack Error

[Greve, Douglas N.,Ph.D.]

It actually looks like it completed and created the desired output file. 
Did you check it? Those errors are generated because it is trying to 
figure out whether the file is a diffusion scan. You can turn it off by 
setting
setenv FS_LOAD_DWI 0
or for bash
export FS_LOAD_DWI=0


On 11/07/2018 09:55 PM, Maryam Tayebi wrote:
>
> External Email - Use Caution
>
> I tried this way, but I got lots of errors, as the attached file. What 
> is the problem? Is there anything wrong with my data? Because I am 
> using the online databases which I think it might be back to 2009 ish.
>
> Thanks
>
> On Thu, 8 Nov 2018 at 11:55, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You have to specify an output directory with -targ and the runs
> you want
> to unpack with -run. See the help (ie, run dcmunpack with -help)
>
> On 11/07/2018 05:38 PM, Maryam Tayebi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer Developers,
> > I was going to reconstruct MPRAGE images from GE 3T machine.
> > First I used this command:
> > /dcmunpack -src . -scanonly scan.log/
> >
> > It made just /scan.log/ file for me. Then I used this command:
> > /unpacksdcmdir -src / -targ  directory>
> > -scanonly scan.log/
> >
> > However, it made 3 files for me; dicomdir.sumfile, parse.status and
> > unpack.log, but they were 0 bites. Furthermore, the following
> message
> > also appeared on the terminal:
> >
> > /ERROR: parsing /hpc/mtay316/tutorial4/practice_with_data/dicoms/
> > See logfile
> /hpc/mtay316/tutorial4/practice_with_data//unpack.log for
> > more details/
> >
> > I used this command for SIEMENS data and it worked. Apparently this
> > code just works on SIEMENS data not GE. So now what is the code
> that I
> > can use for GE dcm images?
> >
> > 1) FREESURFER Version:
> > freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
> > 2) Platform: Ubuntu 16.04 LTS
> > 3) unpack.log : see attached
> >
> > Regards
> >
> >
> > --
> > *Maryam Tayebi*
> >
> > PhD Candidate of Bioengineering
> > Auckland Bioengineering Institute, University of Auckland,
> Auckland,
> > New Zealand
> >
> >
> >
> > MSc of Medical Imaging
> > University of Manchester, Manchester, UK
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> -- 
> *Maryam Tayebi*
>
> PhD Candidate of Bioengineering
> Auckland Bioengineering Institute, University of Auckland, Auckland, 
> New Zealand
>
>
>
> MSc of Medical Imaging
> University of Manchester, Manchester, UK
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] mris_apply_reg failing for area/volume

[Greve, Douglas N.,Ph.D.]

Not sure what is going on. Can you send me the input rh.area file as 
well as lh.40tvs8ref_sym_20.sphere.reg and 
40tvs8ref_sym_20/surf/lh.sphere.reg? You can post them here

https://gate.nmr.mgh.harvard.edu/filedrop2

When it asks you for an email, use gr...@nmr.mgh.harvard.edu and not my 
email above






On 11/08/2018 08:21 AM, James Michael Roe wrote:
>  External Email - Use Caution
>
> Hi Doug
>
> Here is the output file
>
>
> James Michael Roe
> PhD. Candidate
> Center for Lifespan Changes in Brain and Cognition
> Department of Psychology
> University of Oslo
> PB 1094 Blindern
> 0317 Oslo
> Mobile: 958 49 437
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas N.,Ph.D. 
> 
> Sent: 07 November 2018 19:02
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>
> Can you send the terminal output that includes the error?
>
> On 11/06/2018 06:36 PM, James Michael Roe wrote:
>>   External Email - Use Caution
>>
>> Hi Bruce
>>
>> I realise that my last message made it sound as though the problem was fixed.
>> However, I was only confirming that the files load fine in freeview (are not 
>> corrupted) as asked.
>> The issue of many subs area and volume files failing to register when using 
>> --jac is still unsolved
>>
>> Appreciate the support.
>>
>> Thanks
>>
>> James
>>
>> 
>> From: James Michael Roe
>> Sent: 31 October 2018 19:45
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> Hi Bruce
>>
>> Can confirm that both files (rh.area & rh.volume) load fine in freeview
>>
>> Thanks for the help!
>>
>> James
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Bruce Fischl 
>> 
>> Sent: 29 October 2018 15:43
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume
>>
>> Hi James
>>
>> can you verify that the various files (e.g.
>> /cluster/projects/p23/projects/Memory_Project/James/AgeSym/long_recons_FXhemi/010_NDev/1000409_02_10_02_11.long.base_1000409_11/surf/rh.area)
>>
>> are intact by loading them into freeview? For the area file you will of
>> course have to load it as an overlay not as a surface (since it isn't a
>> surface)
>>
>> cheers
>> Bruce
>> On Mon, 29 Oct 2018, James Michael Roe wrote:
>>
>>>   External Email - Use Caution
>>>
>>>
>>> ​Dear freesurfer experts
>>>
>>>
>>>
>>> I’m running the following commands to register RH area and volume files per 
>>> sub to both hemispheres
>>> of a symmetrical template following Xhemi routines.
>>>
>>> The commands have already worked for many subs, but are failing to write 
>>> the target file for a
>>> number of others (and all run fine without the –-jac flag)
>>>
>>>
>>> #right to left
>>>
>>> mris_apply_reg \
>>>
>>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>>
>>> --trg $concatdir/rh.lh.area.${sub}.${template}.nii.gz \
>>>
>>> --streg $SUBJECTS_DIR/$sub/xhemi/surf/lh.${template}.sphere.reg
>>> $SUBJECTS_DIR/${template}/surf/lh.sphere.reg \
>>>
>>> --jac
>>>
>>>
>>>
>>> #right to right
>>>
>>> mris_apply_reg \
>>>
>>> --src $SUBJECTS_DIR/$sub/surf/rh.area \
>>>
>>> --trg $concatdir/rh.rh.area.${sub}.${template}.nii.gz \
>>>
>>> --streg $SUBJECTS_DIR/$sub/surf/rh.${template}.sphere.reg
>>> $SUBJECTS_DIR/${template}/surf/rh.sphere.reg \
>>>
>>> --jac
>>>
>>>
>>>
>>>
>>> The error is not template-specific as the output is the same using 
>>> fsaverage_sym
>>>
>>> Attached is the log file.
>>>
>>>
>>>
>>> Thanks in advance!
>>>
>>>
>>>
>>>
>>> ​- James
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

[Greve, Douglas N.,Ph.D.]

The problem is a combination of things in that mri_tessellate writes out 
a file that read_surf.m cannot read. I have fixed this in our tree. You 
can get around it by using mri_mc instead of mri_tessellate (same exact 
command line). mri_mc uses marching cubes.


On 11/05/2018 01:07 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> Bruce-
>
>
> Thank you for the reply.  I'll try to summarize what I've done (and 
> please see the attached jpeg showing my coordinate examples).
>
>
> I needed to create a surface of the scalp/skull in order to query 
> vertex coordinates in conjunction with some TMS localization.  I ran:
>
>
> mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol
> $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2
> 20 --nhitsmin 2
>
> mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255
> $SUBJECTS_DIR/$sub/surf/lh.seghead
>
> I can load lh.seghead into freeview, cursor onto a vertex and note the 
> coordinates.  I then load the file into matlab via read_surf.  I've 
> since taken care to note that matlab is +1 in vertex number.  I've 
> also ran:
>
>
> mris_curvature -w lh.seghead
>
>
> as you suggested and reread the file in matlab.  Attached are snippets 
> from freeview and matlab showing that when I query lh.pial, I see the 
> correct vertex coordinates in freeview and in matlab.  When I do the 
> same thing but use lh.seghead, the coordinates in matlab no longer 
> match the vertex coordinates that I see in freeview., even after 
> running mris_curvature -w.
>
>
> How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for 
> lh.seghead?  If I load that file into matlab with read_surf, why do my 
> coordinates not match what I see in freeview?
>
>
> -Joel
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> *Sent:* Monday, November 5, 2018 11:12:40 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] [External] Re: Nonsensical Vertex 
> Coordinates, please help with interpretation
> Hi Joel
>
> Doug is on vacation so I'll try to help. You can use mris_curvature -w 
> ...
> to recreate the curv files, but I think that is a red herring. Can you
> summarize what is going on? Have you used mris_info to extract the 
> various
> transforms from the surface file? Did you fix the off-by-one that Doug
> noted?
> cheers
> Bruce
>
>
> On Fri, 19 Oct 2018, Bruss, Joel E wrote:
>
> >
> > External Email - Use Caution
> >
> > Doug-
> >
> >
> > Did you have any other ideas on this?  I'm using FreeSurfer 6.0.0, 
> if that
> > helps any.  I've tried the "mkheadsurf" command on three different 
> subjects
> > and all have the same issues.  The coordinates I get in matlab are 
> nowhere
> > near what I see in Freeview.
> >
> >
> > -Joel
> >
> > 
> 
> > From: Bruss, Joel E
> > Sent: Tuesday, October 16, 2018 3:53:19 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates,
> > please help with interpretation
> >
> > Attached is a screenshot showing what I see in Freeview and what I 
> see in
> > Matlab.
> >
> > 
> 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Greve, Douglas
> > N.,Ph.D. 
> > Sent: Tuesday, October 16, 2018 3:15:16 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates,
> > please help with interpretation
> > which coords are you looking at? They should be the "surface RAS" 
> coords.
> >
> > On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
> > >
> > > External Email - Use Caution
> > >
> > > I couldn't remember if it's 1+ or 1-.  Either way, either direction
> > > give similar coordinates that don't match up to what I can see in
> > > FreeView.
> > >
> > > 
> 
> > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> > >  on behalf of Greve, Douglas
> > > N.,Ph.D. 
> > > *Sent:* Tuesday, October 16, 2018 1:48:14 PM
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* [External] Re: [Freesurfer] Nonsen

Re: [Freesurfer] Multivariable linear regression with binary variables

[Greve, Douglas N.,Ph.D.]

You'd have 512 groups total, which is probably way too many regardless 
of whether you do so manually or automatically. You need to think about 
how you want to model all those variables since modeling all possible 
interactions is not going to be possible.

On 11/08/2018 12:45 PM, Worker, Amanda wrote:
>
> External Email - Use Caution
>
> Hi,
>
>
> I am trying to run a multivariable GLM with mri_glmfit and I am 
> currently setting up my fsgd file. I have 9 binary variables and 1 
> continuous variable. My understanding is that in the fsgd file, my 
> "class" would be every possible combination of these binary variables 
> - which is a lot (hundreds) and setting this up manually doesn't seem 
> reasonable. Is this correct and if so could you recommend another way 
> to run this analysis?
>
>
> Thanks,
>
>
> Amanda
>
>
>
> ___
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Re: [Freesurfer] Multivariable linear regression with binary variables

[Greve, Douglas N.,Ph.D.]

you have to make decisions about which interactions you want to model

On 11/9/18 8:43 AM, Worker, Amanda wrote:

External Email - Use Caution

Yes. I just want to use 7 of those variables as predictors and 2 as covariates 
of no interest in a linear regression model


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: 08 November 2018 18:03:16
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Multivariable linear regression with binary variables

You'd have 512 groups total, which is probably way too many regardless
of whether you do so manually or automatically. You need to think about
how you want to model all those variables since modeling all possible
interactions is not going to be possible.

On 11/08/2018 12:45 PM, Worker, Amanda wrote:
>
> External Email - Use Caution
>
> Hi,
>
>
> I am trying to run a multivariable GLM with mri_glmfit and I am
> currently setting up my fsgd file. I have 9 binary variables and 1
> continuous variable. My understanding is that in the fsgd file, my
> "class" would be every possible combination of these binary variables
> - which is a lot (hundreds) and setting this up manually doesn't seem
> reasonable. Is this correct and if so could you recommend another way
> to run this analysis?
>
>
> Thanks,
>
>
> Amanda
>
>
>
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Re: [Freesurfer] Functional Connectivity in FreeSurfer

[Greve, Douglas N.,Ph.D.]

Yes, see fcseedcor -help

On 11/11/18 4:40 AM, Maedeh Khalilian wrote:

External Email - Use Caution

Dear FreeSurfer experts,
I have a general question, if i have a parcellation(an annotation file e.g 
aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate 
the functional connectivity between the regions(parcels)  using rs-fMRI data?
I mean can I have a 68*68 matrix showing the functional connectivity between 
each pair of regions(parcels) at the end?
I would be grateful if u could help me.
best regards,
Maedeh



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Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

[Greve, Douglas N.,Ph.D.]

It will be in the next release. We may be depricating mris_tessellate in favor 
of mri_mc anyway. But I've already fixed it in mri_tessellate

On 11/9/18 3:31 PM, Bruss, Joel E wrote:

External Email - Use Caution

Doug-


I had time to play around with this, substituted the mri_mc command and 
success!   Thank you so much for resolving this issue.  Is this something that 
will be incorporated into the next release or will I have to remember to run 
this command for any other surfaces that I create?


-Joel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, November 8, 2018 9:26:23 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please 
help with interpretation

The problem is a combination of things in that mri_tessellate writes out
a file that read_surf.m cannot read. I have fixed this in our tree. You
can get around it by using mri_mc instead of mri_tessellate (same exact
command line). mri_mc uses marching cubes.


On 11/05/2018 01:07 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> Bruce-
>
>
> Thank you for the reply.  I'll try to summarize what I've done (and
> please see the attached jpeg showing my coordinate examples).
>
>
> I needed to create a surface of the scalp/skull in order to query
> vertex coordinates in conjunction with some TMS localization.  I ran:
>
>
> mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol
> $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2
> 20 --nhitsmin 2
>
> mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255
> $SUBJECTS_DIR/$sub/surf/lh.seghead
>
> I can load lh.seghead into freeview, cursor onto a vertex and note the
> coordinates.  I then load the file into matlab via read_surf.  I've
> since taken care to note that matlab is +1 in vertex number.  I've
> also ran:
>
>
> mris_curvature -w lh.seghead
>
>
> as you suggested and reread the file in matlab.  Attached are snippets
> from freeview and matlab showing that when I query lh.pial, I see the
> correct vertex coordinates in freeview and in matlab.  When I do the
> same thing but use lh.seghead, the coordinates in matlab no longer
> match the vertex coordinates that I see in freeview., even after
> running mris_curvature -w.
>
>
> How is freeview getting "-79.51, -23.50, -0.50" and vertex #68093 for
> lh.seghead?  If I load that file into matlab with read_surf, why do my
> coordinates not match what I see in freeview?
>
>
> -Joel
>
>
> 
> *From:* 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  on behalf of Bruce Fischl
> <mailto:fis...@nmr.mgh.harvard.edu>
> *Sent:* Monday, November 5, 2018 11:12:40 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] [External] Re: Nonsensical Vertex
> Coordinates, please help with interpretation
> Hi Joel
>
> Doug is on vacation so I'll try to help. You can use mris_curvature -w
> ...
> to recreate the curv files, but I think that is a red herring. Can you
> summarize what is going on? Have you used mris_info to extract the
> various
> transforms from the surface file? Did you fix the off-by-one that Doug
> noted?
> cheers
> Bruce
>
>
> On Fri, 19 Oct 2018, Bruss, Joel E wrote:
>
> >
> > External Email - Use Caution
> >
> > Doug-
> >
> >
> > Did you have any other ideas on this?  I'm using FreeSurfer 6.0.0,
> if that
> > helps any.  I've tried the "mkheadsurf" command on three different
> subjects
> > and all have the same issues.  The coordinates I get in matlab are
> nowhere
> > near what I see in Freeview.
> >
> >
> > -Joel
> >
> >
> 
> > From: Bruss, Joel E
> > Sent: Tuesday, October 16, 2018 3:53:19 PM
> > To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> > Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates,
> > please help with interpretation
> >
> > Attached is a screenshot showing what I see in Freeview and what I
> see in
> > Matlab.
> >
> >
> __