Re: [Freesurfer] aparc+aseg.mgz for network analysis

Thank you all so much! That's great help! I will use Matlab to delete the other labels. Best, Jinsong On Thu, Jul 21, 2016 at 11:48 AM, Douglas N Greve wrote: > That will binarize all the labels, but you could then use that as a mask > > On 07/21/2016 02:46 PM, Bruce Fischl wrote: > > yes,

Re: [Freesurfer] question about image size

Thank you I'll try that. On Thursday, July 21, 2016, Bruce Fischl wrote: > try using the -rl switch in mri_convert. It will "reslice > like" the you give. Give it the 512 volume as > > cheers > Bruce > On Thu, > 21 Jul 2016, Dorsa Haji Ghaffari wrote: > > > Hi, > > I have segmented 288 slices

Re: [Freesurfer] question about image size

try using the -rl switch in mri_convert. It will "reslice like" the you give. Give it the 512 volume as cheers Bruce On Thu, 21 Jul 2016, Dorsa Haji Ghaffari wrote: > Hi, > I have segmented 288 slices of 512x512 dicom MRIs but when I create a mask of > the > left thalamus I get 256 slices o

Re: [Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

How did you create the mask? It should be a surface overlay in fsaverage space, ie, you should be able to view it with tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > Hello freesurfers, > > I would like to use mri_glmfit with --mask but I

[Freesurfer] question about image size

Hi, I have segmented 288 slices of 512x512 dicom MRIs but when I create a mask of the left thalamus I get 256 slices of 256x256 images. Is there any way to get the same number of slices with the same size as I had before? Thank you Dorsa ___ Freesurfer

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

Try using abs instead of pos. abs (absolute) is more appropriate since an F test is unsigned. Also, I would go with a threshold of 2 and not 1.3. I'm just now finding out that such a low threshold can cause a lot of false postives on real data. On 07/21/2016 05:32 PM, Nicola Toschi wrote: > Hi

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

Hi, thanks for your reply. The mri_glmfit-sim was pasted below, here it is the dereferenced version: /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos thanks again, Nicola On 7/21/2016 11:13 PM, Douglas N Greve wrote: > That

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

That is the mri_glmfit command, I need the mri_glmfit-sim. Also, please do not include variables, just the full command with all dereferenced args On 07/21/2016 03:28 PM, Nicola Toschi wrote: > Hi, > > here it is (I also pasted the mri_glmfit line): > > /odir=${prefix}_${meas}_${h}_fwhm${s}_${sur

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

Hi, here it is (I also pasted the mri_glmfit line): /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory// // //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \// //--C ${C1} \// //--glmdir ${odir} --surf fsaverage ${h} ${surf}// // //*/usr/local/freesurfer6dev/bi

Re: [Freesurfer] registering subject pial to fsaverage

Hi Doug Is this what is meant by the example with --help? "Convert the surface coordinates" to me sounds as if it would change the x,y,z of the vertices... Additionally, when I watching the online tutorials surface registration was explained as "aligning the anatomy" so I totally missed that it do

Re: [Freesurfer] aparc+aseg.mgz for network analysis

That will binarize all the labels, but you could then use that as a mask On 07/21/2016 02:46 PM, Bruce Fischl wrote: > yes, that should work also > On Thu, 21 Jul 2016, Koubiyr, Ismail wrote: > >> I think you can use mri_binarize and set the match values as you like. >> Hope it can help. >> >> Bes

Re: [Freesurfer] aparc+aseg.mgz for network analysis

yes, that should work also On Thu, 21 Jul 2016, Koubiyr, Ismail wrote: > I think you can use mri_binarize and set the match values as you like. > Hope it can help. > > Best, > > Ismail > >> On Jul 21, 2016, at 2:13 PM, Jinsong Tang wrote: >> >> Hello freesurfers, >> >> I want to select the subcor

Re: [Freesurfer] aparc+aseg.mgz for network analysis

I think you can use mri_binarize and set the match values as you like. Hope it can help. Best, Ismail > On Jul 21, 2016, at 2:13 PM, Jinsong Tang wrote: > > Hello freesurfers, > > I want to select the subcortical structures (thalamus, pallidum, caudate, > putamen, accumbens, hippocampus, and

Re: [Freesurfer] aparc+aseg.mgz for network analysis

Hi Jinsong you can either copy those labels out into their own volume using mri_extract_label, or use matlab to find the other labels and zero them out cheers Bruce On Thu, 21 Jul 2016, Jinsong Tang wrote: Hello freesurfers, I want to select the subcortical structures (thalamus, pallidum,

[Freesurfer] 'Cerebral Exterior' label in Freeview but not tkmedit

Dear FreeSurfer community, Despite tkmedit being discontinued, I am still using this to make surface edits to my T1s. The main reason is that when I use Freeview and erase skull/dura, Freeview creates this blue label wherever I erase outside of the brain surface. The label is called left (or ri

[Freesurfer] aparc+aseg.mgz for network analysis

Hello freesurfers, I want to select the subcortical structures (thalamus, pallidum, caudate, putamen, accumbens, hippocampus, and amygdala) and the 68 distinct brain regions as nodes of the individual brain networks. The labels are [9,11:13,17:18,26,48,50:54,58, 1002:1035, 2002:2035]. However, in

[Freesurfer] mri_glmfit --mask ERROR: dimension mismatch 1 between y and mask

Hello freesurfers, I would like to use mri_glmfit with --mask but I get this error: dimension mismatch 1 between y and mask. I created a binary mask from 22 aparc labels (using mri_binarize) and I would like to run a surface-based analysis only on those regions. The command I use is: mri_glmfit -

Re: [Freesurfer] registering subject pial to fsaverage

The only thing you are doing with this command is to change the number and identity of the vertices, the xyz will not change at all and so the appearance of the surface will not change (much). On 07/21/2016 01:11 PM, Trisanna Sprung-Much wrote: > Hi Doug > > not quite - I used mri_surf2surf *wit

Re: [Freesurfer] registering subject pial to fsaverage

So if I understand, you used mri_surf2surf to map the curv from your subject to fsaverage. You then viewed the original curv on the original subject and then you viewed the fsaveage-mapped curv on faverage and you find that they are very similar. Is that right? This would not surprise me much.

Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)

what is your mri_glmfit-sim command line? On 07/20/2016 05:56 PM, Nicola Toschi wrote: > Hi List, > > I am getting a couple of strange error when running a 3-group F-test. > > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin > WARNING: 251446 NaNs found in volume > analysis/Ftest/cache.t

Re: [Freesurfer] Subtracting overlays

You can use fscalc (which is a frontend for mris_calc) and handles all file format issues On 07/21/2016 09:35 AM, Bruce Fischl wrote: > Hi Tobias > > yes, mris_calc should do it. If you give the output extension .mgz it > will save in that format instead of curv I believe (and will work fine >

Re: [Freesurfer] Flattening the surface

and 255 is the label that you want to cover? 16G may not be enough. Do you have any machines with more RAM? On Thu, 21 Jul 2016, Younghoon Kim wrote: Hi Bruce, Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the size is about 3000x2000x140. (We obtained this brain image u

Re: [Freesurfer] Flattening the surface

Hi Bruce, Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the size is about 3000x2000x140. (We obtained this brain image using different imaging methods) Our machine has 16GB RAM. Thanks, Younghoon Kim -- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab -

Re: [Freesurfer] registering subject pial to fsaverage

Hi Doug What I mean to say is that the pial surface created by recon-all and the pial surface that has been nonlinearly registered to fsaverage look pretty much identical in sulcal patterns, but I do not understand how this can be the case if one surface has been registered to a surface template b

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Falk yes, it's an active area of devlopment for us cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: Hi Bruce, I thought so. Are there any other means to accelerate this procedure (in the future)? Best, Falk -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Bruce, I thought so. Are there any other means to accelerate this procedure (in the future)? Best, Falk -Ursprüngliche Nachricht- Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 21. Juli 2016 15:52 An: Falk Lüsebrink Cc: Freesurfer support list Betreff:

Re: [Freesurfer] Flattening the surface

is Brain_FS.mgz a segmented volume? How much memory do you have on that machine? On Wed, 20 Jul 2016, Younghoon Kim wrote: Hi Bruce, I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a surface, but received an error message as below: changing type of input vol

Re: [Freesurfer] Combined parcellation of the left and right hemispheres

Hi Varsha try using mri_aparc2aseg cheers Bruce On Thu, 21 Jul 2016, vars...@cns.iisc.ernet.in wrote: > > Hi, > > I've been working on getting a finer parcellation of the Desikan-Killiany > atlas using mris_divide_parcellation. I was able to generate two > annotation files; one each for the lef

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Falk not every part of it is accelerated, but some are cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: Hi Bruce, I'm using the current dev build: ProgramName: mri_ca_label ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/21-13:42:39-GMT BuildTimeSta

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Doug, Zeke, Thank you very much for your help. Best, Ismail On Jul 21, 2016, at 1:15 AM, zkauf...@nmr.mgh.harvard.edu wrote: Current versions of the Mac freesurfer binaries are not compatible with the v5.3 release. Too much has changed since then. If you

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Bruce, I'm using the current dev build: ProgramName: mri_ca_label ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/07/21-13:42:39-GMT BuildTimeStamp: Jul 12 2016 13:31:56 CVS: $Id: mri_ca_label.c,v 1.113 2016/05/13 18:02:49 fischl Exp $ User: luesebrink Machine:

Re: [Freesurfer] Subtracting overlays

Hi Bruce, Great, thanks for the quick reply! That worked beautifully. I was apparently using the wrong output option. Much appreciated! Kind regards, Tobias _ Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imag

Re: [Freesurfer] Subtracting overlays

Hi Tobias yes, mris_calc should do it. If you give the output extension .mgz it will save in that format instead of curv I believe (and will work fine as an overlay) cheers Bruce On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote: Hi,  Is there a way to subtract one surface overlay from ano

Re: [Freesurfer] Freesurfer build stamps do not match

Hi Subin it looks more likely that you just don't have write access to your SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set it and it still points to the one we distribute? Typically you want to set the SUBJECTS_DIR env variable to some other directory where you will

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Falk the dev version of mri_ca_label does use openmp, so should be faster. cheers Bruce On Thu, 21 Jul 2016, Falk Lüsebrink wrote: Hi Bruce, I started the process again with openmp set to 12 using the dev build from 12th July. However, mri_ca_label uses only 1 thread at that point. So I

[Freesurfer] Subtracting overlays

Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias ___

[Freesurfer] Freesurfer build stamps do not match

Hi FreeSurfer Team, After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand: mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Per

[Freesurfer] Combined parcellation of the left and right hemispheres

Hi, I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of th

Re: [Freesurfer] mri_ca_label with high resolution data

Hi Bruce, I started the process again with openmp set to 12 using the dev build from 12th July. However, mri_ca_label uses only 1 thread at that point. So I don't assume any faster processing. Best, Falk -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:fr