Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

I installed matlab and set path of $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox into matlab, but also got the error. What else should I do? Thank you for your always support! On Tue, Dec 2, 2014 at 10:08 AM, zhang mingxia wrote: > Dear freesurfer experts, > > I got this error whe

[Freesurfer] incorrectly labeled vertices in fsaverage lh labels

Hi everyone, In the lh labels of fsaverage (FS 5.3 stable), vertices 102162 and 102163 seem to be incorrectly labeled in lh.cortex.label rather than lh.Medial_wall.label. Anyone noticed this before? I didn't check rh yet. Regards, Vincent. ___

[Freesurfer] relationship between cortical thickness and gyrification index

Dear FreeSurfer users, I have a question regarding the link between cortical thickness and gyrification index: suppose I have a general decrease of cortical thickness in a lobe of the brain. Is it correct to suppose that consiquentely the gyrification index will decrease in the sulci (because of t

[Freesurfer] mri_surfcluster problem

Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.

Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

what happens when you type: which matlab cheers Bruce On Tue, 2 Dec 2014, zhang mingxia wrote: I installed matlab and set path of $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox into matlab, but also got the error. What else should I do? Thank you for your always support! On Tue,

[Freesurfer] Hippocampal subfields

Dear FreeSurfers, I am just finishing a paper using output from Hippocampal subfields and recognized that the current version has been deprecated. I am interested in volumes of the whole hippocampus. Are these volumes still valid and can you estimate when a new version will be available? Can yo

Re: [Freesurfer] Speeding Freesurfer

Francesco, There are ways to speed up single subject processing time by parrallelizing the parts of the recon-all stream that deal with the left and right hemisphere so they get processed simultaneously. This would require a custom script and thus is a bit more complicated than a single call t

Re: [Freesurfer] Hippocampal subfields

Hi Georg, we will be releasing with FreeSurfer 6 a new hippocampal subfield module based on a more accurate atlas built upon ex vivo MRI scans. However, if what you are interested in is the whole hippocampal volume, the results from the new module won't be too different. Cheers, /Eugenio Juan E

[Freesurfer] longitudinal statistics LGI

HI freesurfer experts I have a question about the statistical analysis of longitudinal data. we have run our data through the longtudinal data processing stream. We are looking at the longitudinal effect on the LGI data We are looking at doing a Mixed effects analysis.our main Model Fac

[Freesurfer] T1 weighted versus T2 weighted

Dear FreeSurfer Team, is it possible to run FreeSurfer recon-all on T2-weighted images? Thank you, best, Elisabetta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information i

Re: [Freesurfer] T1 weighted versus T2 weighted

Hi Elisabetta sorry, not at the moment. You can use a T2 in addition to a T1, but not in place of it. Bruce On Tue, 2 Dec 2014, Elisabetta del Re wrote: > > Dear FreeSurfer Team, > is it possible to run FreeSurfer recon-all on T2-weighted images? > Thank you, > best, > Elisabetta > > ___

Re: [Freesurfer] longitudinal statistics LGI

p { margin-bottom: 0.1in; line-height: 120%; }Hi Jon I guess that whenyou say “we have continuous data as to the amount of drug usage”you actually mean that the amount-of-drug-usage is a continuousvariable that changes over time for each subject. So yes you can keepthis variable as a continuous

Re: [Freesurfer] Hippocampal subfields

Hi all, this is really a terrible news! I am writing a paper using hippocampal subfields (ver 5.3). What is the problem with segmentation using this tool? Is it reliable at least on some of the subfield? When will Freesurfer 6 be released? Thank you Angela > Hi Georg, > we will be releasing wit

Re: [Freesurfer] Hippocampal subfields

Hi FS experts, Yes, I'm in the same position and have been trying to do it longitudinally. Does this mean that the outputs are completely unreliable and unstable? Should it be parked until the release of version 6? Thanks Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal Coll

Re: [Freesurfer] T1 weighted versus T2 weighted

Hi Bruce, thank you so much. How would I use T2 in addition to T1 in recon-all? Or can I use T2 only to edit pial surface? Than you again, regards, Elisabetta On Tue, Dec 2, 2014 at 1:07 PM, Bruce Fischl wrote: > Hi Elisabetta > > sorry, not at the moment. You can use a T2 in addition to a T1, b

Re: [Freesurfer] T1 weighted versus T2 weighted

Check the help, but it is something like -T2pial Cheers Bruce > On Dec 2, 2014, at 8:17 PM, Elisabetta del Re > wrote: > > Hi Bruce, > thank you so much. > How would I use T2 in addition to T1 in recon-all? > Or can I use T2 only to edit pial surface? > Than you again, > regards, > Elisabett

Re: [Freesurfer] T1 weighted versus T2 weighted

Hi Bruce, thank you, yes, that is OK. But my question rephrased is whether in my recon-all that I use to start processing, can I input both T1 and T2 together. Thank you again, regards, Elisabetta From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-b

Re: [Freesurfer] T1 weighted versus T2 weighted

I think so, but it will use the T1 only for most of it Cheers Bruce > On Dec 2, 2014, at 8:22 PM, Del Re, Elisabetta > wrote: > > Hi Bruce, > thank you, yes, that is OK. > But my question rephrased is whether in my recon-all that I use to start > processing, can I input both T1 and T2 togeth

Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

Hi Fischl, Thank you. I have resolved the problem by adding the matlab in my path. Mingxia On Tue, Dec 2, 2014 at 9:14 PM, Bruce Fischl wrote: > what happens when you type: > > which matlab > > cheers > Bruce > > On Tue, 2 Dec 2014, zhang mingxia wrote: > > I installed matlab and set path of

Re: [Freesurfer] A question of preproc-sess -fsd

It should be -fsd bold doug On 11/27/14 4:58 AM, zhang mingxia wrote: Dear Freesurfer experts, Could you please give me more detail of "-fsd"? It is asked to "specify a functional subdirectory with -fsd" when i preprocess the functional data. If, for example, the current directory is /home/P

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

You can spec the surface to be pial (instead of the default white). Then spec --projabs to specify the distance into cortex (using negative numbers). doug On 11/27/14 1:24 PM, Kirstie Whitaker wrote: Hi, I was wondering if it's possible to sample x mm from the pial surface using mri_vol2sur

Re: [Freesurfer] convert mgh file to nifti

You can use --proj frac 0 1 .1 See the --help for more info doug On 11/29/14 8:22 PM, Bruce Fischl wrote: > Hi Angela > > that actually looks ok. It should follow the gray/white boundary I > believe. Have you looked at it in the individual subject space without > mapping it to the MNI coords? I t

Re: [Freesurfer] mri_glmfit error

You have a --C that is not followed by a contrast file. doug On 11/26/14 10:58 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, I have been attempting to run the following command in freesurfer v5.3.0: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-gr

Re: [Freesurfer] mri_glmfit error

Thanks Douglas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au

Re: [Freesurfer] ALLvsFIX contrast

No, sorry, I did not expect so many conditions when I wrote mkcontrast-sess 15 years ago :-). I would just write a script to generate the command line. doug On 12/1/14 2:15 AM, Reza Rajimehr wrote: > Hi, > > In an fMRI experiment, I have 60 conditions. I want to make ALLvsFIX > contrast to sel

Re: [Freesurfer] error from selxavg3-sess: matlab:commond not found, ERROR:fast_selxavg3() failed\n

yes, you need matlab installed (octave will work too). On 12/1/14 10:08 PM, zhang mingxia wrote: Does it mean i need to install matlab? On Tue, Dec 2, 2014 at 10:08 AM, zhang mingxia mailto:zhangmingxia1...@gmail.com>> wrote: Dear freesurfer experts, I got this error when I analysis

Re: [Freesurfer] mri_surfcluster problem

That is the right command line. What is the terminal output? On 12/2/14 8:01 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject f

Re: [Freesurfer] mri_surfcluster problem

The command I used is mri_surfcluster --in sig.w --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 30 --sum area100.pos.cluster.summary --o area100.pos.cluster.w --thmin 1.3 Teriminal output is thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 g

Re: [Freesurfer] Speeding Freesurfer

Zeke, Thank you for your prompt response. I've been using for a long time my own bash script that parallelizes the simultaneous computation of the hemisphere-specific steps. Moreover, I re-organized the pipeline for obtaining the pial reconstruction asap. I'm happy to know that next release of Fr