On 1/3/19 5:07 AM, xi star wrote:
>
> External Email - Use Caution
>
> dear experts,
> I try to run FSFAST with a block design paradigm. there a few question
> i can figure out on my own.
> the 1st question:
> the directory structure was set as:
> -meridian
> --sess01
> -
Can you include the full command line (no $variables) and the full
terminal output?
On 1/2/19 4:22 PM, Tamara Sussman wrote:
>
> External Email - Use Caution
>
> Thanks for your response - yes, I should have included this
> information before. :)
>
> $label was set to a label I made by 1
I doubt it would make much difference. If your PET has lots of
extracerebral uptake, then I might use something that has not been skull
stripped (eg, orig.mgz, T1.mgz, nu.mgz). If it does not have much
extracerebral, then using brain.mgz is probably better.
On 12/31/18 10:53 AM, Bruce Fischl w
The contrast is not correct for your design. Your design matrix will
have 3 columns, one for HC, one for CMT, and one for
rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a
DOSS kind of way. If you want to test for a difference in
thickness-meylin slopes between the two groups
you might try this page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
On 12/30/18 1:45 AM, Yerong Li wrote:
> External Email - Use Caution
> Dear FreeSurfer experts:
> I am trying to map ./mri/aparc.a2009s+aseg.mgz and
> ./mri/aparc+aseg.mgz into DTI file.
> Let's say, we
Does that file exist? If not, check to see whether that subject finished
or whether there was an error
On 12/20/18 2:37 PM, 塩浜 直 wrote:
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I'm attempting to do group analysis for cortical thickness map using Qdec GUI.
> We'
T1/lh.glmdir/Hgb_Quad_2StudyCovariates/lh.SuperiorParietal.label
>
> --nonempty --excludeid 0 --avgwf test.dat --sumTest_SupParietal.sum
>
> ERROR: cannot do frame average without input volume
>
> Thank you again for your help!
> Tamara
>
>
> On Thu, Jan 3, 2019 a
Do you have access to the stderr output from this process?
On 1/3/19 3:55 PM, Maksimovskiy, Arkadiy wrote:
>
> Dear Experts,
>
> I was wondering if someone might be able to help diagnose a recon error.
>
> I used the following command to initiate recon:
>
> recon-all -subject RMD002 -i
> /ncf/anl
but otherwise it is safe to do group analysis with v6 tools on individual data
processed with any version of FS
On 1/4/19 12:03 PM, Bruce Fischl wrote:
Hi Mona
if you want to compare with another dataset processed with V6, you probably
have to reprocess everything in this one with V6 too otherw
On 1/4/19 1:27 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurfers
I have a few questions about gammafit flag in mkanalysis-sess command and I
appreciate if you could respond whenever you had time.
-How should we decide which function is best to apply on hemodynamic response
signal? I have used
Class CMT
Variables Age gender
Input fs_VF HC 46 Female
Input fs_RF HC 24 Female
...
My group.diff.mtx should be:
1 -1 0 0 0 0 0
Is it ok?
Thanks a lot
Raffaele
Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> ha scritt
or helping.
To have an only rescaled voxel-wise PET image, these options seem to work only
when -rbv method is used and not -mgx.
Do you know why ?
Best,
Matthieu
Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0
sum.^2 = 1)
On 12/21/18 2:31 PM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Thanks Douglas.
Is there a way to compute a weighted average in one command with fscalc ?
Best,
Matthieu
Le mar. 18 déc. 2018 à 18:03, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>
Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look?
On 1/6/19 6:20 PM, Rusche, Johann wrote:
Dear Freesurfers,
I have been processing my T1 dataset through the longitudinal pipeline with the
-3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large
a
template.reg.lta computed by mri_coreg ? What are the
differences between those different files ?
Best,
Matthieu
Le mar. 18 déc. 2018 à 18:13, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> a écrit :
On 12/7/18 9:29 AM, Matthieu Vanhoutte wrote:
> External Email - Us
Matt
Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing
RBV and MGX? What is your command line? What do you mean that these options
don't seem to work?
.@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 15:01
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_apply_
:
>
> External Email - Use Caution
>
> Thanks for the quick reply. Have sent the file to you now
>
>
> - James
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Grev
did you look at the zero-disparity vs fixation contrast? Can you send
your paradigm file? Can you send pictures?
On 1/9/19 12:26 AM, xi star wrote:
>
> External Email - Use Caution
>
> Hi! FS Experts!
> In the fMRI experiment, there are 2 conditions:
> 1# 3D picture
> 2# zero disparity
On 1/9/19 10:35 AM, Max Owens wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I just wanted to follow up and see if there was anyone who could
> answer my questions:
>
> 1.What is the unit of effect size for the gamma.mgh file created by
> vertexwise GLM Analysis using mri_glmfit?
S
I imagine it will have some systematic effect. If your design is such
that the two scan types are divided across your contrast of interest
(eg, diagnosis), then including it as a nuisance regressor is probably
fine.
On 1/3/19 4:31 PM, Arsenije Subotic wrote:
> External Email - Use Caut
Try raising the threshold
On 1/10/19 1:42 PM, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
>
> Hello ,
> I have results for my mri_glmfit-sim. I find a significant results in
> my cache.th20abs.sig.cluster.summary.
> Yet, the cluster size of the significant cluster is almost t
Yea, the 5.3 stream used FSL brain masking to make the masks for the
fmri. Version 6 uses the FS brain mask transferred into fmri space.
Inevitably, you will have to do a lot of reprocessing. The simplest
thing to do is to delete the mask files in session/bold/masks and
sessoin/bold/RRR/masks (
There should already be two volumes (aparc+aseg.mgz and
aparc.a2009s+aseg.mgz) which you can simply convert to nifti with
mri_convert file.mgz file.nii.gz
On 1/15/19 2:14 PM, Stephanie Hare wrote:
>
> External Email - Use Caution
>
> Good afternoon,
>
> I'm new to Freesurfer; my backgro
What do you mean that the tal volume does not load as a mov volume? Can you
send the terminal output from tkregister2?
On 1/16/19 10:01 AM, Daniel Ferreira wrote:
External Email - Use Caution
Dear Bruce, Martin, and experts,
I posted an issue a few days ago. I have been looking throug
Not sure what you are trying to do, but if you want to check the tal reg of a
typical analysis, you can run
tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --targ
$SUBJECTS_DIR/subject/mri/orig.mgz --ixfm
$SUBJECTS_DIR/subject/mri/transforms/talairach.xfm -outxfm
$SUBJECTS_DIR/subject/mr
Hi Don, have you checked out this web page?
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 1/15/19 7:11 AM, Krieger, Donald N. wrote:
External Email - Use Caution
Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1
coordinates,
I.e. something compa
You can do the analysis in a particular region with masking (--mask
input to mri_glmfit). You can also load the uncorrected overlay into
freeview and adjust the threshold until you get a cluster distribution
you like, then use that threshold in mri_glmfit-sim
On 1/16/19 4:44 PM, Azeez, Azeezat
terinterface {macro,mini,micro}
> %
> Screen: 249 340 (28,28,28), inorm = 1, mov_frame = 0
> Anat: (124 85 127) ( 4.0 -1.0 43.0) 32. 27.7
> Func: (180 -142 42) ( -52.4 -86.4 270.1) OutOfBounds
> --
wishes,
> Kevin
> Date: Tue, 15 Jan 2019 21:47:37 + From: "Greve, Douglas N.,Ph.D."
> Subject: Re: [Freesurfer] preproc-sess mask
> issue To: "freesurfer@nmr.mgh.harvard.edu"
> Message-ID:
> <5b4ea669-5ade-6be4-2435-aed05faf1...@mgh.harvard.edu> C
y black. How
> should I continue from here? If the registration is so far off that it
> is out
> of the field of view, what should I do next?
>
> Thanks
>
> Dani
>
> El mié., 16 ene. 2019 a las 22:54, Greve, Douglas N.,Ph.D.
> (mailto:dgr...@mgh.harvard.edu>>)
atlas measurement applied at the single subject
> level, and I was looking to generate and apply a single binary mask in
> 3D space to all 100 schizophrenia patients' normalized functional
> scans. Any suggestions? I appreciate your input.
>
> Cheers,
>
> Stephanie
Hi Mona, when you run fcseed-config you can specify to use -mean or -pca npca.
-mean produces the mean waveform. -pca will run a PCA on all voxels and take
the first npca components. In principle, using more components will fit more of
the noise. But it can also make the design more poorly cond
What version of FS are you using? version 6 initializes with mri_coreg (the FS
equivalent of spm_coreg). On whole-brain data, I've found this to be very
robust. Is your data whole-brain?
On 1/18/19 5:10 AM, Keri Woods wrote:
External Email - Use Caution
Hi
I have a problem very simila
Use
mri_concat avg-lh-thickness.15.mgh --std --o avg-lh-thickness.15.std.mgh
You can compute mean with --mean instead of --std
On 1/9/19 9:19 AM, Schranzer René wrote:
>
> External Email - Use Caution
>
> Hello everyone,
>
> I have some problems with the computation of the SD of thickness
tru
mri_concat lh.PET.subject1.nii,gz h.PET.subject2.nii,gz
lh.PET.subject3.nii,gz lh.PET.subjectN.nii,gz --mean --o
lh.PET.mean.nii.gz
On 1/11/19 10:37 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> Dear FS experts,
> I resampled PET images for multiple subjects I us
Personally, I think it is fine just to do the average
On 1/11/19 5:00 PM, Arsenije Subotic wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
>
> When calculating global thickness, is it fine to simply use an average
> of lh.thickness and rh.thickness, or is it necessary to weigh
Not for cortical analysis. You might be able to get something useful
from subcortical analysis
On 1/22/19 12:15 PM, Sahnoune,Iman wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I’m writing to ask whether clinical scans with thickness of 5mm are
> currently able to be analyzed usi
You can try mri_binarize with both --erode and --dilate (specifying the
structures with --match and and output surface with --surf). Dilating
then eroding might remove some of the holes (though it is a hack)
On 1/22/19 10:43 AM, Bruce Fischl wrote:
> Hi John
>
> sorry, not really. If you constra
Not sure. Can you tar up the subject and send me the file here
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it
is transferred.
On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
>
> External Email - Use Caution
>
> Hi,
>
> We collected an MP-RAGE scan a
t and told me that user dgreve
> is not valid.
>
> Sorry for the hassle.
>
> François
>
>
>
>
> On 1/22/19, 1:00 PM, "Greve, Douglas N.,Ph.D."
> wrote:
>
> Not sure. Can you tar up the subject and send me the file here
> ftp://
You have effectively applied the registration twice, once when you ran
bbregister to get the output and once when you ran tkregister2 with
--reg. Try that tkrister2 command with func.nii.gz as the --mov
On 1/21/19 6:35 PM, Sam W. wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I h
I don't know what is happening. If the two z-maps are really different,
then it should have given different values. Run this
mri_diff order/z.nii.gz disorder/z.nii.gz
Does it indicate that there is a difference? If so, can you run your two
mri_segment commands and send me the terminal output of e
152
> 20_88 039 0.9905
> 20_88 041 1.0168
> 20_90 049 0.8263
> 20_90 050 1.0208
> 20_95 008 0.8892
> 20_95 010 0.9359
> 20_96 013 0.9191
> 20_96 014 0.9326
> 20_97 008 0.9569
> 20_97 010 0.9731
> 20_98 008 0.9317
&
Can you be more specific about how mri_vol2surf failed? Eg, command
line, terminal output, reason you think it did not work
On 1/21/19 10:47 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> Dear FS experts,
> I have a statistical map from the output of a surface based analysi
You are going about it in the right way. Not sure about a better
template. You could create the surfaces on an individual and then apply
a linear transform to get it into fsaverage space. Again, another hack ...
On 1/22/19 1:56 PM, john Anderson wrote:
> External Email - Use Caution
>
>
Is grf.th1.3.pos.sig.cluster.mgh in the mni152 2mm space? You should
check the registration with
tkregister2 --mov grf.th1.3.pos.sig.cluster.mgh --reg
$FREESURFER_HOME/average/mni152.register.dat --surfs
It looks like you projected it to the white surface of fsaverage
On 1/22/19 2:08 PM, john An
aution
>
> Thanks Greve. The output is attached now.
>
>
> Emanuel
>
>
> On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> can you include the full terminal output?
>
> On 12/13/18 7:45 AM, Emanuel Alv
On 1/22/19 2:59 PM, Hatton, Sean wrote:
> External Email - Use Caution
>
> Hi all,
>
> Two quick questions:
>
> 1. Is there an expected timeframe for when FreeSurfer 6.1 (or next version)
> is published?
Not a firm date. We have started the process to release a new version.
Last time,
Can you send the full terminal output and/or the log file?
On 1/22/19 2:53 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer developers,
>
> I was following the functional connectivity walkthrough for resting
> stage BOLD data and I got the attached error when I
try this one
http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx
On 1/22/19 7:47 PM, Peters, Douglas G wrote:
>
> External Email - Use Caution
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
>
>
> Error Message:
>
>
> Not Found
>
> The requested URL /pub/docs/freesurfer.group
r/bin/mris_fwhm)
On 1/23/19 10:11 AM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> Attached is the log file.
>
> On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Can you send
not
> perfect, while others are very bad.
>
> I've checked the subjectname file for some subjects with poor
> registration (eg 20_101), and they are correct.
>
> Thanks,
> Keri
>
> On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> mailto:
Hi John, I would recommend that you use permutation. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
In terms of the threshold, "not going higher than .01" means using
between 0 and .01 (eg, don't use .05). For permutation, you can use
whatever thershold you
Version 6 does not work very well with such high-res data. I created a
patch for the HCP that you can download from here
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp
This works in version 6. Just follow the instructions in the README.
I ran it on your data, and it looks pr
You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum
Note use "lh" even if it is the entire cerebellum as FS commands
generally require a hemisphere.
The run mri_vol2surf specifying --hemi lh --surf cerebellum
On 1/23/19 10:04 AM, john Anderson wrote:
>
> External E
It should only do that if you have specified a projection fraction. Is
that your full command line? Can you send the full terminal output?
On 1/24/19 4:56 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve, I appreciate your guidance very much.
>
> I followed your s
I downloaded the patch
> and will rerun the scans using version 6.
>
> Thanks,
> François
>
>
> On 1/24/19, 3:40 PM, "Greve, Douglas N.,Ph.D."
> wrote:
>
> Version 6 does not work very well with such high-res data. I created a
>
e only thing linking the anatomical and functional images?
Thanks very much, you've helped me a lot. Now I just have to go and see where I
mixed up the files!
Thanks again,
Keri
On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Can you tar u
Hi Amrita, can you just paste the text into the email?
thanks
doug
On 1/25/19 10:51 AM, Amrita Bedi wrote:
External Email - Use Caution
Hi Dr Greve,
Ran mris_fwhm and got the attached.
On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
mri_info will do it. If you just want the orientation string, you can
add --orientation. Or do you still want the interpretation of the matrix?
On 1/25/19 10:10 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> I think that mri_info will try to figure this out and tell you (in the
> "Orientation" output).
I don't see anything.
On 1/25/19 11:56 AM, Amrita Bedi wrote:
External Email - Use Caution
[X]
Here you go.
On Friday, January 25, 2019, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
Hi Amrita, can you just paste the text into the email?
thanks
doug
On 1/
Those are the commands. Can you send the command lines you used and a fuller
description of exactly how it is not working?
On 1/25/19 10:56 AM, Boris Rauchmann wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I´m trying to extract the cortical thickness of individuals fro
Many thanks in advance for helping.
Best,
Matthieu
Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> a écrit :
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
I used the following command to obtain only rescaled voxel-wi
l if you explain how does it interpret from matrix.
>
> Thanks,
> Ritesh Mahajan
>
> ----- Original Message -
> From: "Greve, Douglas N.,Ph.D."
> To: "freesurfer"
> Sent: Friday, January 25, 2019 10:26:47 PM
> Subject: Re: [Freesurfer] Orientation by
If you intend to use one of the aseg structures, then they are the same.
On 1/28/19 10:14 AM, Matthieu Vanhoutte wrote:
External Email - Use Caution
Hi Douglas,
Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> a écrit :
On 1/25/19 7:57 AM, Ma
This is probably an incorrectly fixed defect. Look at the tutorial for fixing
defects. Basically, you need to look at the wm.mgz volume in that area and
manually fix the segmentation errors that caused the defect.
On 1/28/19 11:25 AM, Erika Portera wrote:
External Email - Use Caution
G
Can you be more specific?
On 1/28/19 2:12 PM, Jahan, Bushra wrote:
Hi,
I'm wondering which column in the FreeSurfer summary file represents the
cluster size for the cortical and subcortical clusters.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.
that should work
On 1/28/19 2:44 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I am trying to project a subcortical volume , that I manually made, from
fsaverage to individual subject's space.
I was wondering if it's ok if I use mri_vol2vol for this purpose. I copied my
command below:
; copy and paste the text directly into the email. This is
> *much* more useful for us.
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Amrita Bedi wrote:
>
>
> External Email - Use Caution
>
>
>
Can you just paste the message rather than attaching an image?
On 2/4/19 11:33 AM, Jordan Fowler wrote:
>
> External Email - Use Caution
>
> I have recently installed the free surfer software and when testing
> that it is installed correctly using the examples listed on the
> website I g
rfully.
>
> Thanks!
> François
>
>
> On 1/24/19, 7:34 PM, "Greve, Douglas N.,Ph.D."
> wrote:
>
> The dev version has the same problem :(
>
> On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote:
> > External Email
Can you send all the things that mri_glmfit suggests sending?
On 2/6/19 5:16 AM, Michal Tanzer wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I’m attempting to compute mri_glmfit to correlate cortical thickness
> with my dependent var while controlling for ag
First, you'll have to find the closest vertex for each point in
fsavarage. You can do this with by creating a label file then using
mri_label2label with the --paint option.
To find the label associated with each vertex, it is probably easiest
to use matlab using read_surf.m and read_annotation
have you seen this description of coordinate systems?
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 2/5/19 11:47 AM, ts...@rcmd.org wrote:
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I have a raw nifti file created from a stack of DICOM scanner images
The way it works is that it goes through each vertex in the label and
finds the vertex that is closest on the target surface and assigns that
value to that vertex. I think what is happening here is that two of the
source vertices are both closest to a single target vertex. In this
case, the val
fore volume
> to surface projection, how would you deal with it ?
>
> Best,
> Matthieu
>
>> Le 28 janv. 2019 à 17:41, Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>
>> If you intend to use one of the aseg structu
On 1/29/19 11:21 AM, Adam Martersteck wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer team,
> I have two comments/questions about PET PVC & Doug’s 2016 Neuroimage
> paper:
>
> 1) It looks like the 2 rigid transforms created during mri_gtmpvc
> found at [$pvc_directory/aux/anat
On 2/4/19 7:26 PM, Daniel Leopold wrote:
>
> External Email - Use Caution
>
> Hi all,
>
> I'm hoping to get some input on clustering, multiple correction,
> smoothing preferences, and (if available) best practices. Please
> correct me if I'm wrong, but it seems that the amount of attent
If you want to test it out yourself, you can get it from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/
On 2/4/19 6:09 AM, Glasser, Matthew wrote:
>
> External Email - Use Caution
>
> There is a little more testing we are doing.
>
> Matt.
>
> From: Shachar Gal mailt
Looking at the help, it looks like it will produce a separate file for
each run for each session. Is that what you want?
On 2/1/19 9:41 AM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfers
>
>
> Hi
>
>
> I have been doing seed to seed connectivity analysis using fcseedcor.
>
> I have multiple run
It might be a little more accurate, but my guess is that it will not
make much of a difference.
On 1/30/19 2:01 PM, Matthieu Vanhoutte wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer’s experts,
>
> I have read the paper from Marcoux, et al. « An Automated Pipeline for
> the A
mris_fwhm)
>
> ans =
>
> 1
>
> Do you think this error has to do with the version of matlab I am
> using perhaps?
>
> Best
> Amrita
>
>
> On Tuesday, January 29, 2019, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>
The cluster summary file should indicate which vertex is the maximum.
You can then go into matlab and run
y = MRIread('y.mgh');
v = squeeze(y.vol(vertexno+1,1,1,:));
where y.mgh is the input to mri_glmfit (ie, the stack of all your
subjects) and vertexno is the vertex number from the cluster summ
I have not. Can you send the recon-all.log file?
On 2/1/19 6:01 PM, Morgan Botdorf wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> I recently ran recon-all on data using the T2pial flag to improve the
> pial surface (using version 6.0). The T2 images seemed to improve the
> pia
On 1/25/19 7:52 AM, Klaas Bahnsen wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> First of all: Thank you so much for your work and your fantastic product.
>
> I turn to you with a short question, I hope it is not too unnecessary
> and can be answered quickly.
>
Are you using fspalm? If so, there should be a something.y.ocn.dat file
that has the mean thickness for each subject and cluster
On 2/8/19 6:16 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
>
> Dear Freesurfer Developers,
> I'm using PALM to run permutation analyses to correct
not sure what you want. MNI coords for each lesion?
On 2/8/19 7:21 AM, Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
Hi Freesurfer devs,
I saw that Freesurfer export measures of hypointensities. I was wondering if
it´s possible to know where are located this brain l
It will not used trilinear interp. Try it with nearest neighbor
On 2/10/19 11:55 AM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
>
> Dear Douglas,
>
> Before using "mri_gtmpvc --psf 0 --no-tfe -- rbv" according your advice to
> obtain voxel-wise output rescaled without PVC c
All the white matter in the cerebrum (so all white matter excluding WM
in cerebellum, brainstem, or diencephalon). We have changed the name to
CerebralWhiteMatterVol
On 2/11/19 10:37 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
>What is the meaning of the
can you send the full mri_surf2surf terminal output?
On 2/11/19 8:08 AM, ?? wrote:
>
> ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I didn't cache the data during recon-all, so I ran the
>
> >following:
>
> >
>
> > ?0?2?0?2?0?2?
This is the purpose of fsplam. fspalm is just a frontend for palm meant
to produce the output your would have gotten if you had run
mri_glmfit-sim. If you don't want to run fspalm, then look inside it for
the commands that do this.
On 2/11/19 9:05 AM, C.P.E. Rollins wrote:
> External E
2 segmentations
> Computing statistics for each segmentation
>
> Reporting on 2 segmentations
> Using PrintSegStat
> Computing spatial average of each frame
> 0 1
> Writing to lh.V2dorsal_AB_orderVsdisorder_avg
> 0 0.119339
> 1 -1.93788
> mri_segstats done
>
&g
.edu>
>
>
> >Date: Thu, 7 Feb 2019 22:29:43 +
> >From: "Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu>>
> >Subject: Re: [Freesurfer] zero values when run recon-all with T2pial
> > flag (V6.0)
> >To: "freesurfer@
it would be helpful if you were to tell us exactly what you were doing
(eg, URL, which text box, etc)
On 2/13/19 3:49 PM, Peng Wang wrote:
>
> External Email - Use Caution
>
> Please help!
>
> Repost with a better title.
>
> ___
> Freesurfer mai
can you send the command line without the variables?
On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>
> External Email - Use Caution
>
> Thanks for pointing that out! Unfortunately after making the change
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj
il.com>_
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
-6298
>
>
> On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <mailto:ddcc2...@gmail.com>> wrote:
>
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> -
Remove the backslashes
On 2/14/19 10:15 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021
> \ --so $SUBJECTS_DIR/0021/surf/lh.white
> $SUBJECTS_DIR/0021/surf/lh.thickness \ --so
> $SUBJECTS_DIR/0021/sur
Are you going to do an FIR analysis or are you going to assume a shape
to the hemodynamic response function? If you are assuming the shape (the
usual), then the answer to both of your questions is no
On 2/14/19 8:31 AM, Rockhill, Alexander P. wrote:
> Hello Freesurfer experts,
>
> I am workin
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