[Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

Hi Dr. Greve, Thank you very much for getting back to me so promptly. If memory serves me right, I am pretty sure that the orientations were incorrect in tkmedit but will double check soon. Based on what you are saying and based on what I read in the wiki about mri_convert it seems that I will be

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

Thanks! I will take your advice and start to learn it. I appreciate your help so much!! Elissa On Tue, Mar 22, 2016 at 6:28 PM, Bruce Fischl wrote: > something like: > > > set SUBJECTS = (subject1 subject2 ... subject60) > foreach s ($SUBJECTS) >foreach hemi (lh

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

something like: set SUBJECTS = (subject1 subject2 ... subject60) foreach s ($SUBJECTS) foreach hemi (lh rh) mris_anatomical_stats -l $hemi.BA45.label $s $hemi end end definitely worth taking the time to learn! It will save you endless amounts of time in the longrun and it's

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

Thanks! I am a newbie so I think it would take me longer to learn how to write the script then to just do it one at a time! :) On Tue, Mar 22, 2016 at 6:23 PM, Bruce Fischl wrote: > oh, no, but write a script to do it! That's what unix is for. > > On Tue, 22 Mar >

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

oh, no, but write a script to do it! That's what unix is for. On Tue, 22 Mar 2016, Elissa Ash wrote: > Thanks Bruce > I am calculating the thickness for a given ROI (rh.BA45.label) and comparing > it > across subjects and it is tedious to have to type in the command separately > each time >

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

Thanks Bruce I am calculating the thickness for a given ROI (rh.BA45.label) and comparing it across subjects and it is tedious to have to type in the command separately each time (~60 subjects). I was hoping that there was a way to input multiple subjects at once. That's it. Thanks, Elissa On

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

Hi Elissa not really. What would you want it to do? There are tools for tabulating the output of mris_anatomical_stats across subjects, if that's what you are trying to do cheers Bruce On Tue, 22 Mar 2016, Elissa Ash wrote: > > Dear experts, > > Is there any way to run the

[Freesurfer] mris_anatomical_stats on more than one subject at a time?

Dear experts, Is there any way to run the mris_anatomical_stats command on more than one subject at a time? Thanks, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel

Re: [Freesurfer] mris_flatten error

Dear. All. I tried tksurfer and it works.. It's still very strange why tksurfer-sess does not work. The command line that worked successfully is: tksurfer replay06 lh inflated -curv -gray Then I overlayed the contrast result sig.nii.gz and the registration file. Then I cut the plane and then

Re: [Freesurfer] PET voxelwise

That looks ok, but if you want to do a group analysis, you can add --trgsubject fsaverage and the output surface will be in fsaverage space. You can then concatenate the data together (mri_concat) into one stack and then run mri_glmfit etc for your group analysis. You may or may not want to

Re: [Freesurfer] cannot allocate memory

The problem is not the command, it is the size of the data it generates. You can try reducing the size of the anatomical to a bounding box around the brain. This is a bit tricky as you also have to compute a new registration. I can help step you through the process if you want to go in that

Re: [Freesurfer] Surface based analysis using FA maps

I don't know of a reference where someone has done this (though I would be surprised if it is not out there), so just be aware of this if you try to publish. The commands look correct, however, you may or may not want to sample in the middle of the cortical ribbon (--projfrac 0.5). Since this

Re: [Freesurfer] mri_glmfit-sim ( cluster wise analysis)

answers below On 03/22/2016 11:03 AM, Alshikho, Mohamad J. wrote: > > Dear FS experts, > > I ran cortical thickness analysis as previously explained in Wiki : > > Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > > My data is previously cached so I ran the command :

Re: [Freesurfer] Using digital tablet pen

Thank you so much Lilla ! On Tue, Mar 22, 2016 at 12:29 PM, Lilla Zollei wrote: > > Hi Mahmoud, > > At the below link you will find some suggestions / settings that we use > with our Cintiq tablet: > > >

Re: [Freesurfer] mris_flatten error

Oh, I see. I showed the contrast results on a surface using the command: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower Then I select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then,

Re: [Freesurfer] Regarding: oblique view

Hello Bruce, Thanks again for your prompt response. We have an official holiday here. Will send the info on Thursday. Thanks and regards, Sampada Predoctoral student KGMU, Lko India On haveay, March 2016, Bruce Fischl wrote: > I see > > if you have defects that

Re: [Freesurfer] mris_flatten error

then you must not have cut the patch from those surfaces. The error is about a vertex # in the patch (147220), which is larger than the total number of vertices in those surfaces (144977), so it's out of bounds. How did you do the cutting? On Tue, 22 Mar 2016, Ji Won Bang wrote: Oh, I see.

Re: [Freesurfer] mris_flatten error

Oh, I see. When I run all of these surfaces, it gave me the exactly same numbers... [jbang@cpu156 surf]$ mris_euler_number lh.inflated euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total

[Freesurfer] PET voxelwise

Hi Freesurfer Community, I am trying to run a vertex-wise analyses of PET data. I have already performed bbregister. Next, I did mri_vol2surf for each subject, left and right hemispheres. for i in `cat subjects`; do mri_vol2surf --src FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out

Re: [Freesurfer] Regarding: oblique view

I see if you have defects that large you should look at the inflated.nofix surface to see what they are. What is your voxel resolution? cheers Bruce On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and

Re: [Freesurfer] Regarding: oblique view

Thanks Bruce for your reply. I did run it thru' recon-all. It went for more than 2 days and then exited with XL defect error (convex hull was more than 14000 and vertex size about 54000). So today I started by running the recon-all in parts. I did not find anything wrong with brainmask files after

Re: [Freesurfer] mris_flatten error

no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not a surface - it's a scalar field over the surface. The ones that should be the same are: lh.inflated lh.white lh.pial lh.orig lh.sphere lh.sphere.reg and same for the rh (but different from the lh ones) cheers Bruce

Re: [Freesurfer] mris_flatten error

Dear. Bruce. Thanks for your help. When I tried: mris_euler_number rh.inflated.K It gave me: nquads=15728644, nvertices=574 ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices! Probably trying to use a scalar data file as a surface! When I tried: mris_euler_number

Re: [Freesurfer] Using digital tablet pen

Hi Mahmoud, At the below link you will find some suggestions / settings that we use with our Cintiq tablet: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations "Segmenting using a Cintiq tablet or display" Best, Lilla On Tue, 22 Mar 2016,

Re: [Freesurfer] mris_flatten error

you can try recon-all -make all for that subject and and see if it doesn anything. But run mris_euler_number on those surfaces and see if they match. They should all have the same number of faces/edges/vertices (for one hemisphere in the same subject) On Tue, 22 Mar 2016, Ji Won Bang wrote:

Re: [Freesurfer] mris_flatten error

Dear. Bruce. Thank you for your advice. I think I misunderstood what you meant. What I did is this. I showed the contrast result on a surface by using the command: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast HorVer Then I cut line, and then plane (occipital

Re: [Freesurfer] cannot allocate memory

Hi Doug, Thanks for your response. What I'm trying to do is to get each voxel's times course in structural space and I was under the impression that mri_vol2vol --mov func.nii would be the right way to go. Would you please let me know what the best way would be to do this? best, Ehsan,. On

Re: [Freesurfer] mris_flatten error

what surface did you recut it from? Can you run mris_euler_number on that surface (presumably the inflated) and also on the white/orig/pial surfaces? They should all have the same number of vertices, but I suspect some of them won't, meaning that they need to be regenerated. cheers Bruce

[Freesurfer] mris_flatten error

Dear. Freesurfer experts. Hi. How are you? I'm trying to flatten the visual cortex using the command mris_flatten (freesurfer version 5.3.0). The command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat The error

Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

Hi Bruce, Again, thank you for the quick response! I will be looking forward to the upgrade then. Kind regards Morten -Oprindelig meddelelse- Fra: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce Fischl Sendt: 22. marts 2016

Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

Hi Morten not yet. The STN is on our list of things to segment (as is the SN), although both will likely require good T2* (or maybe T2) weighted images. cheers Bruce On Tue, 22 Mar 2016, Morten Sejer Hansen wrote: Dear Bruce, Thank you for your quick and precise answer. One last

Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

Dear Bruce, Thank you for your quick and precise answer. One last question. Is it possible to segment the Nucl. Subthalamicus? It is a subcortical anatomical structure, and is a part of the basal ganglia. It is not included in the output following the command: asegstats2table --subjects

[Freesurfer] Using digital tablet pen

Dear Experts, I was wondering if someone could share with me and others the experience using digital tablet pen and those sort of things instead of mouse to edit and touch the images especially the masks. I appreciate your help. Thank you! Mahmoud ___

[Freesurfer] Surface based analysis using FA maps

Dear FS experts, I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands: 1. I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold

[Freesurfer] mri_glmfit-sim ( cluster wise analysis)

Dear FS experts, I ran cortical thickness analysis as previously explained in Wiki : Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target

Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

To check whether the orientation is correct, you can view it in freeview or tkmedit. When you click on the axial view it should show up axially, etc. Though you cannot tell whether it is left-right reversed this way. You cannot feed it a matrix, but you can specify the direction cosines on the

Re: [Freesurfer] Create a surface overlay with statistic results using AAL ROI

There is not an easy way to do this. You'd have to make an annotation from the AAL. Possible, but not easy. On 3/21/16 3:54 PM, carolina.mr wrote: Hi all, I have some statistical results for AAL 90 coordinates (correlation coefficients from network measurements x clinical data). I would like

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

try now On 3/21/16 10:24 PM, Bharadwaj, Pradyumna - (prad) wrote: > Hi Doug, > > Could you please upload epidewarp.fsl for FSL 5.x once again. > > Thanks! > -Prad > > From: freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] extracting pial surface area numbers...

That number is the mean vertex area, so to get the total area for each subject multiply that number by the number of vertices in the cluster. On 3/21/16 2:29 PM, Karl Liu wrote: Dear FS team, My question is how I should extract the measure of pial surface area from a significant cluster

Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

Hello Sampada, Because of significant changes in the code, we halted development of the beta release I sent you last year. We will be publishing a new beta release soon (week-ish) but in the meantime, if you want the latest "dev" version of the freesurfer you can downlownd it from our Download

Re: [Freesurfer] Regarding: oblique view

sure. Have you tried running it through recon-all? It may work fine On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > Thanks Bruce for your reply. The acquisition was oblique and the voxel size > doesn't > conform to the 1mm cube isotropic. I am trying to work on it and figure out a >

Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

Thanks Bruce. I was sent the link for dev version by Zeke last year. It's working on Linux platform. But, I am not able to download or install it on Mac. Thanks and kind regards, Sampada On Tuesday, March 22, 2016, Bruce Fischl wrote: > Hi Sampada > > V6 is not

Re: [Freesurfer] Regarding: oblique view

Thanks Bruce for your reply. The acquisition was oblique and the voxel size doesn't conform to the 1mm cube isotropic. I am trying to work on it and figure out a solution. However, if I am not, hope its okay to send you the nifti image. Thanks and regards, Sampada Rnday, March 20, 2016, Bruce

Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

Hi Morten the insula you should be able to get out of the cortical labels in the various *.annot files. The substantia nigra we don't segment at the moment, and I suspect it would be hard to do so from only a T1-weighted scan. cheers Bruce On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:

Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

Hi Sampada V6 is not out yet, although we are actively (frantically?) working on it. cheers Bruce On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > Dear freesurfer experts, > > I am trying to do hippocampal subfields segmentation on Mac. I will greatly > appreciate if freesurfer 6.0 version link

[Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

Dear Experts, I am interested in retrieving the volume of the insula and substantia nigra from T1W structural scans converted to nii.gz files. All scans have undergone the recon-all process without error. I have seen volume estimations of Insula and substantia nigra performed in several

Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix

Sorry, I forgot to mention that I went back to the original line 51 of the Marie Schaer code in "make_outer_surface". No "fix" anymore. Marco 2016-03-16 11:51 GMT+02:00 Marco Bucci : > Dear all, > > I forward again my original post. > I also attach the recon-all.log of