date:20170804

Re: [Freesurfer] Co-ordinate systems in FS

2017-08-04 Thread Douglas Greve


Add --no-fixmni to the mri_surfcluster command


On 8/4/17 3:03 PM, Martin Juneja wrote:

Hi Douglas,

When I checked the summary created by FreeSurfer by running FS commands:

For cortical gyrification I get (here co-ordinates are in TalX TalY 
and TalZ):


# ClusterNo  Max   VtxMax   Size(mm^2) *TalX   TalY   TalZ *   NVtxs   
 WghtVtx   Annot
   1   -2.108   44783   1067.81-28.3   -0.4 41.8   2111   
 -3503.03  caudalmiddlefrontal
   2   -1.837   87895505.11-29.8  -85.0  1.6724   
 -1114.00  lateraloccipital
   3   -1.731   60125335.00-24.1   38.5 27.8541 
-799.69  rostralmiddlefrontal
   4   -1.660  157315236.93-20.1  -60.7 52.0529 
-766.88  superiorparietal
   51.457   79262 93.31-45.72.4  -17.9173 
 237.80  superiortemporal
   6   -1.440   34463 88.73-46.93.8 41.2170 
-231.97  precentral


For cortical thickness I get (here co-ordinates are in MNIX MNIY and 
MNIZ):
# ClusterNo  Max   VtxMax   Size(mm^2) *MNIX   MNIY   MNIZ *   CWP 
 CWPLowCWPHi   NVtxsWghtVtx   Annot
   16.658  102251   3976.09-42.7   -8.6 54.9  0.00020 
 0.0  0.00040   923419027.15  precentral
   23.368   44083   3096.64-28.8  -43.8  -17.3  0.00020 
 0.0  0.00040   5273 7856.00  fusiform
   32.808  156481   1476.57-64.4  -30.5  2.8  0.00818 
 0.00659  0.00978   3169 4837.73  superiortemporal



Command to save these summaries were as following:

For gyrification: mri_surfcluster --in sig.mgh --subject fsaverage 
--hemi lh --surf white --annot aparc  --thmin 1.3 --sum 
LH_Perform_LGI.summary1.3
For thickness: mri_glmfit-sim --glmdir xyz --cache 1.3 neg --cwp 0.05 
--2spaces


Before these, I used general FS commands: mris_preproc, mri_surf2surf 
and mri_glmfit for both.


Only difference is I did not run mri_glmfit-sim on gyrification 
measures but ran this on thickness, area and volume measures due to 
orthogonal/non-orthogonal differences between gyrification and 
(thickness, area and volume) measures.


Thanks.


On Fri, Aug 4, 2017 at 11:24 AM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


How do you know one is MNI and one it Tal? can you send a summary
of your commands?


On 8/4/17 2:09 PM, Martin Juneja wrote:

Hi FreeSurfer experts,

I am trying to correlate my behavioral data with whole brain
cortical measures using cortical measures as IVs and behavioral
data DV.

Somehow the significant clusters I get from cortical thickness,
area and volume are in MNI co-ordinates but significant clusters
from local gyrification-behavioral data are in Talairach
co-ordinates.

I used identical procedures to preprocess my data but still I am
getting my results in different co-ordinate systems (thickness,
volume, area in MNI and gyrification in Tal).

I would really appreciate any help.
MJ


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Re: [Freesurfer] label2annot issue

2017-08-04 Thread Redwan Maatoug

Doug, did you receive my files?
I received an email explaining that the mail is too big and I need to wait
for an authorisation from the moderator.

Thank you,
Redwan


On Aug 4, 2017 10:34 AM, "Redwan Maatoug"  wrote:

> Thank you very much Doug, I really appreciate your help and your patience,
>
> General purpose : in total I have 112.*nii* that I tried to convert them
> to 112.*mgh* files and then to combined them in a *.annot* file with
> different colors.
>
> FIRST ISSUE :
> When I have converted the files from volumetric to surface, I have used
> this command line :
> *mri_vol2surf --mov parcel_1.nii **--reg MNI152_T1_brain.dat --hemi lh
> --o **parcel_1.mgh*
>
> So this command line worked for 60 files on 112 files but for some of them
> (for example *parcel_1.nii*) after the conversion the .MGH file seems to
> be empty.
>
> Because when I use the command line mri_surfcluster to extract the
> coordinates of the vertices :
> (*mri_surfcluster --in parcel_1.mgh --hemi lh --subject fsaverage --thmin
> 0 --nofixmni --olab parcel_1.mgh*) the label file is empty.
>
> when I want to display the .MGH file with the following command line I do
> not see anything :
> *tksurfer fsaverage lh inflated -overlay parcel_1.mgh **-fminmax .5 1 *
>
> BUT when i display the .NIFTI file like that :
> *tkmeditfv fsaverage orig.mgz -overlay parcel_1.nii **-surfs -fminmax .5
> 1*
> I see something
>
> First could you tell me why for some files I can convert them from .NII to
> .MGH but not for all of them.
>
> SECOND ISSUE :
> For the files, I have successfully converted (because with mri_surfcluster
> I have vertices coordinates in the label files : like parcel_97.mgh and
> parcel_100.mgh), could you please tell the steps to follow to display a
> combined .annot file on tksurfer.
>
> Please find attached :
> -parcel_1.nii (issue to convert from .nii to .mgh)
> -parcel_1.mgh (I have the feeling that it is empty)
> -brain template in MNI 152 space I have used for mri_vol2surf
> -parcel_97.mgh and parcel_100.mgh (i can't display them as a combined
> .annot file in tksufer)
> -the ctab with all the colors for the different parcels.
>
> Thank you very very much,
> Redwan
>
> On Fri, Aug 4, 2017 at 9:52 AM, Douglas Greve 
> wrote:
>
>> Yes, send me two label files and the ctab again.
>>
>> On 8/4/17 12:49 PM, Redwan Maatoug wrote:
>>
>> Hi Douglas,
>>
>> I tried to rename the parcel files and in the ctab but it does not change
>> anything. I have the feeling that sometime label2abnot can read the colors
>> because as you can see in the screenshots there is some colors on the
>> brain.
>> If I give you the files could you help me to follow the rights steps to
>> make? Maybe I am missing something but I really need this to be done to
>> compare the résultats in fMRI and in EEG.
>>
>> Thank you very much,
>> Redwan
>>
>> On Aug 3, 2017 15:40, "Douglas N Greve" 
>> wrote:
>>
>>> that would mean that mris_label2annot is probably not reading any of
>>> your labels because it is expecting the label name to be, eg,
>>> lh.parcel_1.mgh-0001.label.label based on what you have told me. Try
>>> changing he label name in the folder to lh.parcel_1.mgh-001.label and
>>> change the ctab names to parcel_1.mgh-0001
>>>
>>>
>>> On 08/03/2017 06:35 PM, Redwan Maatoug wrote:
>>> > In the Yeo_split_surf/ the label have exactly the same names as in the
>>> > ctab.
>>> >
>>> > They are named like that :
>>> > parcel_1.mgh-0001.label
>>> > parcel_2.mgh-0001.label
>>> > parcel_3.mgh-0001.label
>>> > ...
>>> > parcel_112.mgh-0001.label
>>> >
>>> > Yes we had to split the Yeo_split_surface because the goal was to do
>>> > some analyzes in fMRI and EEG using the same atlas. We had to split
>>> > the atlas when for example the ROI was crossing the medial line etc...
>>> >
>>> > But now I just want to combine the files again so it is not supposed
>>> > to have overlapping no ?
>>> >
>>> > Thank you,
>>> > Redwan
>>> >
>>> > On Thu, Aug 3, 2017 at 3:21 PM, Douglas N Greve
>>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>> >
>>> > It may have to do with the label names that get created from the
>>> ctab.
>>> > What are the names of the labels in Yeo_split_surf/ ? I can't
>>> > figure out
>>> > what you are doing with that code. Looks like you have broken the
>>> yeo
>>> > atlas into labels, then you're combining them together again?
>>> >
>>> >
>>> > On 08/03/2017 05:57 PM, Redwan Maatoug wrote:
>>> > > Thank you ffor your quick answer,
>>> > >
>>> > > I have attached the --ctab
>>> > >
>>> > > Here is the link for the .mgh files.
>>> > >
>>> > > https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE
>>> > 
>>> > >
>>> > >
>>> > > So my command line to extract the coordinates from the .mgh
>>> files :
>>> > >
>>> > > *I)*
>>> > > for f in ${1}/*.mgh
>>> > > do
>>> > > mri_surfcluster --in ${f} --hemi

Re: [Freesurfer] ROI labeling?

2017-08-04 Thread Sadie Marvel

Sorry, I meant that I would somehow want to merge all of these masks together 
into one. Not changing the values in the masks, but somehow combining them. 
Also, with the mri_glmfit --label flag, is it possible to have multiple labels 
listed (like one label per subject)?
Sort of like a frame mask where we we want to take into account every subject's 
individual ROI label.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Thursday, August 3, 2017 4:55 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ROI labeling?

what do you mean by an average of the mask? Such an average would not be
binary.


On 08/03/2017 04:30 PM, Sadie Marvel wrote:
> And what if I wanted to compute just one ROI mask (for each region) that is 
> an average of all the subjects individual ROI masks?
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, August 3, 2017 4:15 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] ROI labeling?
>
> If you are just going to use them as a mask for mri_glmfit, then you can
> just pass it as --mask or --label, no need to map it back to the
> individual (which you could do with mri_surf2surf)
>
>
> On 08/03/2017 04:08 PM, Sadie Marvel wrote:
>> Hi again Freesurfers,
>>
>> I am doing a surface based ROI analysis where for each subject,
>> isomorphic ROIs of 300 vertices (centered around peak functional
>> activations) were found on the fsaverage surface space. I was
>> wondering if I should register these masks that I have created back to
>> each subject's individual surface before creating labels for these
>> ROIs, and if so, what would the registration file be to register the
>> fsaverage space back to each subject's space? The goal of this is to
>> be able to run mri_glmfit on just the spaces within these labels. Is
>> there a better method? Also, each subject will have a different number
>> of labels considering that not every ROI was present on every subject.
>> will this be a problem when running glmfit?
>>
>> Thanks
>>
>>
>>
>>
>>
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Re: [Freesurfer] Co-ordinate systems in FS

2017-08-04 Thread Martin Juneja

Hi Douglas,

When I checked the summary created by FreeSurfer by running FS commands:

For cortical gyrification I get (here co-ordinates are in TalX TalY and
TalZ):

# ClusterNo  Max   VtxMax   Size(mm^2)  *TalX   TalY   TalZ *   NVtxs
 WghtVtx   Annot
   1   -2.108   44783   1067.81-28.3   -0.4   41.8   2111
 -3503.03  caudalmiddlefrontal
   2   -1.837   87895505.11-29.8  -85.01.6724
 -1114.00  lateraloccipital
   3   -1.731   60125335.00-24.1   38.5   27.8541
-799.69  rostralmiddlefrontal
   4   -1.660  157315236.93-20.1  -60.7   52.0529
-766.88  superiorparietal
   51.457   79262 93.31-45.72.4  -17.9173
 237.80  superiortemporal
   6   -1.440   34463 88.73-46.93.8   41.2170
-231.97  precentral

For cortical thickness I get (here co-ordinates are in MNIX MNIY and MNIZ):
# ClusterNo  Max   VtxMax   Size(mm^2)  *MNIX   MNIY   MNIZ *   CWP
 CWPLowCWPHi   NVtxsWghtVtx   Annot
   16.658  102251   3976.09-42.7   -8.6   54.9  0.00020
 0.0  0.00040   923419027.15  precentral
   23.368   44083   3096.64-28.8  -43.8  -17.3  0.00020
 0.0  0.00040   5273 7856.00  fusiform
   32.808  156481   1476.57-64.4  -30.52.8  0.00818
 0.00659  0.00978   3169 4837.73  superiortemporal


Command to save these summaries were as following:

For gyrification: mri_surfcluster --in sig.mgh --subject fsaverage --hemi
lh --surf white --annot aparc  --thmin 1.3 --sum LH_Perform_LGI.summary1.3
For thickness: mri_glmfit-sim --glmdir xyz --cache 1.3 neg --cwp 0.05
--2spaces

Before these, I used general FS commands: mris_preproc, mri_surf2surf and
mri_glmfit for both.

Only difference is I did not run mri_glmfit-sim on gyrification measures
but ran this on thickness, area and volume measures due to
orthogonal/non-orthogonal differences between gyrification and (thickness,
area and volume) measures.

Thanks.


On Fri, Aug 4, 2017 at 11:24 AM, Douglas Greve 
wrote:

> How do you know one is MNI and one it Tal? can you send a summary of your
> commands?
>
> On 8/4/17 2:09 PM, Martin Juneja wrote:
>
> Hi FreeSurfer experts,
>
> I am trying to correlate my behavioral data with whole brain cortical
> measures using cortical measures as IVs and behavioral data DV.
>
> Somehow the significant clusters I get from cortical thickness, area and
> volume are in MNI co-ordinates but significant clusters from local
> gyrification-behavioral data are in Talairach co-ordinates.
>
> I used identical procedures to preprocess my data but still I am getting
> my results in different co-ordinate systems (thickness, volume, area in MNI
> and gyrification in Tal).
>
> I would really appreciate any help.
> MJ
>
>
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Re: [Freesurfer] Co-ordinate systems in FS

2017-08-04 Thread Douglas Greve

How do you know one is MNI and one it Tal? can you send a summary of 
your commands?



On 8/4/17 2:09 PM, Martin Juneja wrote:

Hi FreeSurfer experts,

I am trying to correlate my behavioral data with whole brain cortical 
measures using cortical measures as IVs and behavioral data DV.


Somehow the significant clusters I get from cortical thickness, area 
and volume are in MNI co-ordinates but significant clusters from local 
gyrification-behavioral data are in Talairach co-ordinates.


I used identical procedures to preprocess my data but still I am 
getting my results in different co-ordinate systems (thickness, 
volume, area in MNI and gyrification in Tal).


I would really appreciate any help.
MJ


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[Freesurfer] Co-ordinate systems in FS

2017-08-04 Thread Martin Juneja

Hi FreeSurfer experts,

I am trying to correlate my behavioral data with whole brain cortical
measures using cortical measures as IVs and behavioral data DV.

Somehow the significant clusters I get from cortical thickness, area and
volume are in MNI co-ordinates but significant clusters from local
gyrification-behavioral data are in Talairach co-ordinates.

I used identical procedures to preprocess my data but still I am getting my
results in different co-ordinate systems (thickness, volume, area in MNI
and gyrification in Tal).

I would really appreciate any help.
MJ
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Re: [Freesurfer] Optseq2 onset times

2017-08-04 Thread Douglas Greve


those are not concerning, you can just round to the nearest TR


On 8/4/17 12:32 PM, Ruthie Shaffer wrote:

Hi,

I’m using Optseq2 to generate stimulus / jitter schedules, and, 
depending on the TR used, in the output timing files I see several 
event onset times very close to the correct time, but slightly off 
(for example, something like 124.7999, instead of 124.8).  I’ve used 
the following command to generate timing files:


optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 
--nkeep 6 --o CRtiming.2017 --nsearch 10 --tnullmin 0 --tnullmax 6.4



Should I be concerned about optimal onset times that are slightly off 
from the actual possible onset times based on the TR, or is it correct 
to assume it should be 124.4, instead of 124.4001 or 125.8, instead of 
125.7999, for example?


Thank you in advance for any help on this!

Best wishes,

Ruth Shaffer





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Re: [Freesurfer] label2annot issue

2017-08-04 Thread Douglas Greve


Yes, send me two label files and the ctab again.


On 8/4/17 12:49 PM, Redwan Maatoug wrote:

Hi Douglas,

I tried to rename the parcel files and in the ctab but it does not 
change anything. I have the feeling that sometime label2abnot can read 
the colors because as you can see in the screenshots there is some 
colors on the brain.
If I give you the files could you help me to follow the rights steps 
to make? Maybe I am missing something but I really need this to be 
done to compare the résultats in fMRI and in EEG.


Thank you very much,
Redwan

On Aug 3, 2017 15:40, "Douglas N Greve" > wrote:


that would mean that mris_label2annot is probably not reading any of
your labels because it is expecting the label name to be, eg,
lh.parcel_1.mgh-0001.label.label based on what you have told me. Try
changing he label name in the folder to lh.parcel_1.mgh-001.label and
change the ctab names to parcel_1.mgh-0001


On 08/03/2017 06:35 PM, Redwan Maatoug wrote:
> In the Yeo_split_surf/ the label have exactly the same names as
in the
> ctab.
>
> They are named like that :
> parcel_1.mgh-0001.label
> parcel_2.mgh-0001.label
> parcel_3.mgh-0001.label
> ...
> parcel_112.mgh-0001.label
>
> Yes we had to split the Yeo_split_surface because the goal was to do
> some analyzes in fMRI and EEG using the same atlas. We had to split
> the atlas when for example the ROI was crossing the medial line
etc...
>
> But now I just want to combine the files again so it is not supposed
> to have overlapping no ?
>
> Thank you,
> Redwan
>
> On Thu, Aug 3, 2017 at 3:21 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>> wrote:
>
> It may have to do with the label names that get created from
the ctab.
> What are the names of the labels in Yeo_split_surf/ ? I can't
> figure out
> what you are doing with that code. Looks like you have
broken the yeo
> atlas into labels, then you're combining them together again?
>
>
> On 08/03/2017 05:57 PM, Redwan Maatoug wrote:
> > Thank you ffor your quick answer,
> >
> > I have attached the --ctab
> >
> > Here is the link for the .mgh files.
> >
> >
https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE

>   
 >
> >
> >
> > So my command line to extract the coordinates from the
.mgh files :
> >
> > *I)*
> > for f in ${1}/*.mgh
> > do
> > mri_surfcluster --in ${f} --hemi lh --subject fsaverage
> --thmin 0
> > --nofixmni --olab ./${f}
> > done
> >
> > _#OUTPUT for 1 file #_
> > Reading source surface
> > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
> > Done reading source surface
> > Computing metric properties
> > Loading source values
> > number of voxels in search space = 163842
> > Done loading source values (nvtxs = 163842)
> > overall max = 1 at vertex 0
> > overall min = 0 at vertex 1
> > surface nvertices 163842
> > metric props tot surface area 65416.984375
> > group_avg_vtxarea_loaded 1
> > masked surface area 82219.390625
> > NOT Adjusting threshold for 1-tailed test
> > thminadj = 1
> > Searching for Clusters ...
> > thmin=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
> > minarea=5.00
> > Found 3 clusters
> > Max cluster size 4759.318359
> > thsign = abs, id = 0
> > version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42
> zkaufman
> > Exp $
> > hemi   = lh
> > srcid  = Yeo_Split_surf/parcel_9.mgh
> > srcsubjid  = fsaverage
> > srcsurf= white
> > srcframe   = 0
> > thsign = abs
> > thmin  = 1
> > thmax  = -1
> > fdr= -1
> > minarea= 5
> > xfmfile= talairach.xfm
> > nth = -1
> > subjectsdir= /usr/local/freesurfer/subjects
> > FixMNI = 0
> > - XFM matrix (RAS2RAS) ---
> >
>   
 /usr/local/freesurfer/subjects/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;

Re: [Freesurfer] label2annot issue

2017-08-04 Thread Redwan Maatoug

Hi Douglas,

I tried to rename the parcel files and in the ctab but it does not change
anything. I have the feeling that sometime label2abnot can read the colors
because as you can see in the screenshots there is some colors on the
brain.
If I give you the files could you help me to follow the rights steps to
make? Maybe I am missing something but I really need this to be done to
compare the résultats in fMRI and in EEG.

Thank you very much,
Redwan

On Aug 3, 2017 15:40, "Douglas N Greve"  wrote:

> that would mean that mris_label2annot is probably not reading any of
> your labels because it is expecting the label name to be, eg,
> lh.parcel_1.mgh-0001.label.label based on what you have told me. Try
> changing he label name in the folder to lh.parcel_1.mgh-001.label and
> change the ctab names to parcel_1.mgh-0001
>
>
> On 08/03/2017 06:35 PM, Redwan Maatoug wrote:
> > In the Yeo_split_surf/ the label have exactly the same names as in the
> > ctab.
> >
> > They are named like that :
> > parcel_1.mgh-0001.label
> > parcel_2.mgh-0001.label
> > parcel_3.mgh-0001.label
> > ...
> > parcel_112.mgh-0001.label
> >
> > Yes we had to split the Yeo_split_surface because the goal was to do
> > some analyzes in fMRI and EEG using the same atlas. We had to split
> > the atlas when for example the ROI was crossing the medial line etc...
> >
> > But now I just want to combine the files again so it is not supposed
> > to have overlapping no ?
> >
> > Thank you,
> > Redwan
> >
> > On Thu, Aug 3, 2017 at 3:21 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > It may have to do with the label names that get created from the
> ctab.
> > What are the names of the labels in Yeo_split_surf/ ? I can't
> > figure out
> > what you are doing with that code. Looks like you have broken the yeo
> > atlas into labels, then you're combining them together again?
> >
> >
> > On 08/03/2017 05:57 PM, Redwan Maatoug wrote:
> > > Thank you ffor your quick answer,
> > >
> > > I have attached the --ctab
> > >
> > > Here is the link for the .mgh files.
> > >
> > > https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE
> > 
> > >
> > >
> > > So my command line to extract the coordinates from the .mgh files :
> > >
> > > *I)*
> > > for f in ${1}/*.mgh
> > > do
> > > mri_surfcluster --in ${f} --hemi lh --subject fsaverage
> > --thmin 0
> > > --nofixmni --olab ./${f}
> > > done
> > >
> > > _#OUTPUT for 1 file #_
> > > Reading source surface
> > > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
> > > Done reading source surface
> > > Computing metric properties
> > > Loading source values
> > > number of voxels in search space = 163842
> > > Done loading source values (nvtxs = 163842)
> > > overall max = 1 at vertex 0
> > > overall min = 0 at vertex 1
> > > surface nvertices 163842
> > > metric props tot surface area 65416.984375
> > > group_avg_vtxarea_loaded 1
> > > masked surface area 82219.390625
> > > NOT Adjusting threshold for 1-tailed test
> > > thminadj = 1
> > > Searching for Clusters ...
> > > thmin=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
> > > minarea=5.00
> > > Found 3 clusters
> > > Max cluster size 4759.318359
> > > thsign = abs, id = 0
> > > version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42
> > zkaufman
> > > Exp $
> > > hemi   = lh
> > > srcid  = Yeo_Split_surf/parcel_9.mgh
> > > srcsubjid  = fsaverage
> > > srcsurf= white
> > > srcframe   = 0
> > > thsign = abs
> > > thmin  = 1
> > > thmax  = -1
> > > fdr= -1
> > > minarea= 5
> > > xfmfile= talairach.xfm
> > > nth = -1
> > > subjectsdir= /usr/local/freesurfer/subjects
> > > FixMNI = 0
> > > - XFM matrix (RAS2RAS) ---
> > >
> > /usr/local/freesurfer/subjects/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;
> > > 
> > > Reading source surface
> > > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
> > > Done reading source surface
> > > Computing metric properties
> > > Loading source values
> > > number of voxels in search space = 163842
> > > Done loading source values (nvtxs = 163842)
> > > overall max = 1 at vertex 4422
> > > overall min = 0 at vertex 0
> > > surface nvertices 163842
> > > metric props tot surface area 65416.984375
> > > group_avg_vtxarea_loaded 1
> >

[Freesurfer] Optseq2 onset times

2017-08-04 Thread Ruthie Shaffer

Hi,

I’m using Optseq2 to generate stimulus / jitter schedules, and, depending on 
the TR used, in the output timing files I see several event onset times very 
close to the correct time, but slightly off (for example, something like 
124.7999, instead of 124.8).  I’ve used the following command to generate 
timing files:

optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 --nkeep 6 
--o CRtiming.2017 --nsearch 10 --tnullmin 0 --tnullmax 6.4

Should I be concerned about optimal onset times that are slightly off from the 
actual possible onset times based on the TR, or is it correct to assume it 
should be 124.4, instead of 124.4001 or 125.8, instead of 125.7999, for example?

Thank you in advance for any help on this!

Best wishes,

Ruth Shaffer



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Re: [Freesurfer] Pineal gland volume?

2017-08-04 Thread Douglas Greve

Yes, you will need to choose an index and then pass the color table to 
mri_segstats with --ctab to make sure it appears in the output.



On 8/4/17 10:25 AM, Bruce Fischl wrote:

Hi Rotem

sorry, we don't label the pineal gland, but yes you can label it in 
the volume yourself using freeview. I think if you add it to the color 
lut file it will be included in the stats, but perhaps Doug can comment

Bruce


On Fri, 4 Aug 2017, Rotem Saar wrote:


Dear Freesurfer experts,

I wondered if its possible to extract the volume of the pineal gland 
using the

basic cortical + sub-cortical segmentation (recon-all)?

I could not find the volume of this ROI in the output.

If the volume output for this ROI is available - please guide me 
where to look

(maybe I missed it?)

If not - does manual ROI drawing and following,volume calculation is 
possible

using freesurfer?

Thanks !

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work
Ashkelon Academic College, Ashkelon, 78211

Israel






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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Pineal gland volume?

2017-08-04 Thread Bruce Fischl


Hi Rotem

sorry, we don't label the pineal gland, but yes you can label it in the 
volume yourself using freeview. I think if you add it to the color lut file 
it will be included in the stats, but perhaps Doug can comment

Bruce


On Fri, 4 Aug 2017, Rotem Saar wrote:


Dear Freesurfer experts,

I wondered if its possible to extract the volume of the pineal gland using the
basic cortical + sub-cortical segmentation (recon-all)?

I could not find the volume of this ROI in the output.

If the volume output for this ROI is available - please guide me where to look
(maybe I missed it?)

If not - does manual ROI drawing and following,volume calculation is possible
using freesurfer?

Thanks !

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work
Ashkelon Academic College, Ashkelon, 78211 

Israel


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Re: [Freesurfer] output with input matrix size and referential

2017-08-04 Thread pierre deman-kibleur

it seems to works thanks.

On Wed, Aug 2, 2017 at 6:20 PM, Douglas Greve 
wrote:

> Try adding --to-scanner to the mris_convert command. I think you'll need v6
>
>
> On 8/2/17 12:02 PM, pierre deman-kibleur wrote:
>
> yes, it's what i wanted to say.
>
> On Aug 2, 2017 17:46, "Douglas Greve"  wrote:
>
> what do you mean by referential? the coordinate system of the vertex
> coords?
>
> On 8/2/17 4:49 AM, pierre deman-kibleur wrote:
>
> Hi,
>
> Is it possible to have the gifti output in the same referential as the
> orig nii file as well ?
> I tried mris_convert lh.white  lh.white.gii -rl mri/orig/001.mgz
> but mris_convert doesn't have the -rl option.
>
> Regards,
> Pierre
>
> On Wed, Aug 10, 2016 at 2:40 PM, Iglesias, Eugenio 
> wrote:
>
>> You can always run mri_convert with the -rl (“reslice like”) flag to
>> achieve this. Something like: mri_convert input.mgz output.mgz -rl
>> reference.mgz -odt float
>> If it’s a segmentation volume, you should add -rt nearest, in order to
>> use nearest neighbor interpolation.
>> Cheers,
>> Eugenio
>>
>> Juan Eugenio Iglesias
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 10 Aug 2016, at 13:31, pierre deman  wrote:
>>
>> Hello,
>>
>> I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal
>> subfield etc ...
>> in a matrix with the same size as the input of recon-all (and not the
>> cubic matrix 256x256x256) and with the same orientation.
>>
>> what is the best way to do it ?
>>
>> Cheers,
>> Pierre
>>
>> --
>> DEMAN Pierre
>> Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094>
>> ___
>> Freesurfer mailing list
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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 you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>> ___
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>>
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>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
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>> HelpLine at
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>> in error
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>> properly
>> dispose of the e-mail.
>>
>>
>
>
> --
> DEMAN Pierre
> Mobile : +33 7 82 57 80 94 <+33%207%2082%2057%2080%2094>
>
>
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-- 
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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Re: [Freesurfer] Co-ordinate systems in FS

Re: [Freesurfer] label2annot issue

Re: [Freesurfer] ROI labeling?

Re: [Freesurfer] Co-ordinate systems in FS

Re: [Freesurfer] Co-ordinate systems in FS

[Freesurfer] Co-ordinate systems in FS

Re: [Freesurfer] Optseq2 onset times

Re: [Freesurfer] label2annot issue

Re: [Freesurfer] label2annot issue

[Freesurfer] Optseq2 onset times

Re: [Freesurfer] Pineal gland volume?

Re: [Freesurfer] Pineal gland volume?

Re: [Freesurfer] output with input matrix size and referential

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