[Freesurfer] FreeSurfer downloading

Hi there, This is SAHIL BAJAJ, a postdoc fellow from Houston Methodist Research Institute. I have been trying to download Freesurfer for my linux machine but somehow the link on the website- http://freesurfer.net/fswiki/Download is not opening, I would really appreciate any help. Thanks, Sahil

[Freesurfer] Segmentation fault: Core dumped

I checked the segmentation of anatomical data (generated using recon-all), and it looks fine to me. Here I am also attaching the log file created when I run this command. Any help would be really appreciated. Thanks, Sahil -- ----- Sahil Bajaj Post-docto

[Freesurfer] Cortical thickness using freesurfer

here. I would really appreciate any help. Thanks, Sahil -- ----- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. Office: 713

[Freesurfer] Cortical thickness last step

sing --reshape-factor 7 in step 4 also but still I get exactly same error after running step 5. Could you please help me in figuring out this problem? Thanks, Sahil -- ----- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Depa

[Freesurfer] Using qdec to view cluster results

7;t display any cluster results in terminal window. If I do everything from very first step, starting from loading table.dat, creating design once again, everything is working fine. I would really appreciate any help. Thanks, Sahil -- --------- Sahil Baja

[Freesurfer] Cortical thickness average

then average over those but I would rather prefer to average over 100 lh.thickness.fsaverage.mgh files first and then calculate thickness for each ROI to get 11 text files. Any help would be really appreciated. Thanks, Sahil -- - Sahil Bajaj Post

Re: [Freesurfer] Cortical thickness average

t; 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.

[Freesurfer] Qdec interface issue

. The thing is it was working before for some time, then after a computer crash, it no longer works. We replaced the video card but are still experiencing the same problem. At this point I would welcome any suggestions. Thanks, Sahil -- -- - Sahil

[Freesurfer] ROIs2Label

e help me to figure out what I am doing wrong here? Also, how can I view the label in FreeView i.e. is there any way to load this new label just like LookUp Table? Thanks, Sahil -- - Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer&#x

[Freesurfer] Normalization for functional connectivity

Thanks, Sahil -- --------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.br...@gmail.com ___ Fre

Re: [Freesurfer] Normalization for functional connectivity

eg > ROI.mgz -segid 1 ...) > > On 05/10/2016 10:37 AM, Sahil Bajaj wrote: > > Hello all, > > > > I am interested in importing some seed regions which are in MNI space > > in order to calculate functional connectivity maps. Looks like command > > prepr

Re: [Freesurfer] Normalization for functional connectivity

connectivity little far from the seed regions which are in subject-wise anatomical space. On Wed, May 11, 2016 at 3:08 PM, Martin Juneja wrote: > I would suggest you to check if preproc is done using the argument > -mni-305-2mm. > > On Wed, May 11, 2016 at 12:48 PM, Sahil Bajaj > wr

[Freesurfer] Connectivity from external seeds

Sahil -- -- - Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.br...@gmail.com ___ Freesurfer mailing list

[Freesurfer] Binary images multiplication

. Thanks, Sahil -- -- - Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.br...@gmai

[Freesurfer] ROIs in midline for cortical thickness

Hi everyone, I have supplementary motor area (SMA) defined in standard MNI volume space and I would like to extract cortical thickness for this area. I have 80% of SMA in left hemisphere and 20% on right hemisphere. So I am stuck at the command mri_vol2surf before proceeding to mri_segstats. In m

Re: [Freesurfer] ROIs in midline for cortical thickness

and right surfaces and draw your ROIs that way. > > cheers > > Bruce > On Wed, 1 Feb 2017, Sahil Bajaj wrote: > > Hi Dr. Fischl, >> Thank you so much for your reply. >> >> I have this SMA activation from a fMRI task. I am interested in getting >> cortical thic

Re: [Freesurfer] Error viewing corrected results

Hello Martin and Antonin, I was following this conversation very closely to understand how to use PALM in FreeSurfer. Can any of you please confirm in case I am interested in checking correlation between gyrification index (LGI) and behavioral measure using two tailed, p < 0.05: Step 1: I used --

Re: [Freesurfer] Error viewing corrected results

which is very unexpected in my > > data set. > > > > So basically I really doubt if I am running the stats correctly because > > PCC > > looks high at that big cluster (shown in PCC in attached screen shot). > > > > Could you please suggest if there is any al

Re: [Freesurfer] Error viewing corrected results

old > > > > it by your cluster-forming threshold (I suppose that you should > > correctly > > > > convert z value to t-value), to see your initial clusters after > > > > thresholding". > > > > > > > > Thanks a lot Antonin. > > > > Sahi

[Freesurfer] Contrast matrix for PVR

Hi everyone, >From FreeSurfer manual and discussion forum, I found that volume and LGI can be correlated using mri_glmfit command with -pvr flag. For that, my fsgd file has age, gender as covariates and the file is as following: GroupDescriptorFile 1 Class Male Class Female Variables Age Inp

[Freesurfer] Eklund's 2016 and FreeSurfer

Hi, I was wondering if there is any paper published by FreeSurfer team or FreeSurfer experts (after Eklund's 2016 paper) stating that the cluster failure issue is not an issue in FreeSurfer toolbox and/or whether CFT of less than 0.05 or 0.01 to estimate cortical thickness/volume/area maps is fine

Re: [Freesurfer] Eklund's 2016 and FreeSurfer

ischl wrote: > Hi Sahil > > Doug has a paper submitted on this topic and will probably respond soon, > but give him a couple of days due to Thanksgiving > > cheers > Bruce > > > On Wed, 22 Nov 2017, Sahil Bajaj wrote: > > Hi, >> I was wondering if the

[Freesurfer] Subjectwise extraction from ROIs

Hello experts, I identified two clusters (X for thickness and Y for volume) showing significant association between cortical measures (thickness and volume) and motor-performance. I followed steps from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and got several output

[Freesurfer] Fwd: Subjectwise extraction from ROIs

Hello everyone, I was wondering if someone could please help me in figuring out following issues. Thanks a lot, Sahil -- Forwarded message -- From: Sahil Bajaj Date: Thu, Feb 15, 2018 at 3:50 PM Subject: Subjectwise extraction from ROIs To: Freesurfer support list Hello

Re: [Freesurfer] Fwd: Subjectwise extraction from ROIs

Dear Dr. Greve, I have following follow-up questions ('red' colored) for you and would really appreciate any help. On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve wrote: > sorry for the delay, thanks for reposting > > > On 02/20/2018 11:33 AM, Sahil Bajaj wrote: > &g

[Freesurfer] ICV bias in CV measures

External Email - Use Caution Dear FS experts, This paper was published in 2013: https://www.sciencedirect.com/science/article/pii/S1053811913007064?via%3Dihub#s0040 I was just wondering if the current version of FreeSurfer can still introduce bias in cortical volume measures if I

[Freesurfer] How to run GLM FIT simulation in parallel?

External Email - Use Caution Hello experts, I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 abs --cwp 0.05 --2spaces command, but its taking forever even if I reduce # of permutations from 1000 to 10. I was just wondering if there’s a version of FreeSurfer f

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

ong to run. How many input > subjects do you have? > > On 12/06/2018 12:55 PM, Sahil Bajaj wrote: > > > > External Email - Use Caution > > > > Hello experts, > > > > I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 >

Re: [Freesurfer] How to run GLM FIT simulation in parallel?

: > I think something is wrong if you only have 45 subjects, it should not > take that long. Can you send your mri_glmfit command line and the > terminal output of mri_glmfit-sim? > > On 12/06/2018 01:14 PM, Sahil Bajaj wrote: > > > > External Email - Use Caution

[Freesurfer] mri glm fit matrix is ill-conditioned

External Email - Use Caution Hi experts, I am running following command: mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

[Freesurfer] Unable to run recon all

External Email - Use Caution Hello FS experts, I am trying to run recon all on about 100 subjects. But one out of 100 subjects finishes recon all with error, and doesn't complete the process. Here I am attaching recon all log for your reference. Also, before installing freesurfer

Re: [Freesurfer] Unable to run recon all

quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > > On 1/6/20 11:49 AM, Sahil Bajaj wrote: > > > > External Email - Use Caution > > > > Hi Dough, > >

Re: [Freesurfer] Unable to run recon all

:50 AM Sahil Bajaj wrote: > Hi Dough, > > I just uploaded one of the files on Martinos Center File Drop > <https://gate.nmr.mgh.harvard.edu/filedrop2/>. I hope that works ! > (Somehow, uploading through ftp was taking too long). > > Thanks. > > On Mon, Jan 6,

[Freesurfer] CORONA Research study in India - an online survey !

://www.boystownhospital.org/research/faculty/sahil-bajaj Given the seriousness of the disease, I would really appreciate if you can contribute to scientific research related to COVID-19. Thanks a lot ! Best, Sahil -- - *Sahil** Bajaj, Ph.D.* Director

[Freesurfer] Job opportunity (ResearchAssistant/Lab Manager) at Boys Town National Research Hospital

questions/queries, please contact:* *Sahil Bajaj, PhD* Director Multimodal Clinical Neuroimaging Laboratory (MCNL) E-mail: sahil.ba...@boystown.org *&* *James Blair, PhD* Director, Center for Neurobehavioral Research E-mail: james.bl...@boystown.org *About Boys Town:* Boys Town has been chan

[Freesurfer] FreeView issue!

External Email - Use Caution Hi everyone, I am having following error while opening freeview in terminal: BT136080:01_Project_FreeSurfer bajsah$ freeview -f fsaverage/surf/lh.inflated /Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation fault: 11 $FREESURFER_

Re: [Freesurfer] FreeView issue!

Wang, Ruopeng wrote: > What if you run: > > $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f > fsaverage/surf/lh.inflated > > > On Jul 16, 2021, at 1:07 PM, Sahil Bajaj wrote: > > > > External Email - Use Caution > > > > > > Hi

Re: [Freesurfer] FreeView issue!

External Email - Use Caution Hi, I reinstalled FreeSurfer and now the latest version i.e., 7.2.0, but somehow I am still getting the same error message, please see below. I am still unsure how can I fix this issue? Last login: Wed Jul 21 12:43:52 on ttys003 freesurfer-d

[Freesurfer] Job opportunity (ResearchAssistant) at Boys Town National Research Hospital

External Email - Use Caution Please apply at https://secure-web.cisco.com/1yo0ekSWIR0Yp45MZ3-6sWQmS9wHjqoQSAfI0CL1kuo7zD1QzqmlDkaj9B1kr2X90yA4Q58HRFrSjAkMk2UTjx1-Q5FXHVZ8WMP2pxkZZtOWtbs3lfjplX4AZzPzOWvEaQ5yy_5CEyALTIAWDE6mT6aJjbFoW-GQA-P0tXPfIHJHWOPwMJ27NuNxG-QXEhHYMbSlgoa1EVA0jVIa

[Freesurfer] Faces and vertices error !

External Email - Use Caution Hi FreeSurfer community, I am trying to map subject-specific cortical thickness map to standard fsaverage space and I ran the following command where sub1_filled is my individual subject in native: mri_surf2surf --srcsubject sub1_filled --srcsurfreg t

[Freesurfer] Problem with FreeSurfer 8.0

External Email - Use Caution Greetings, I am trying to use the latest FreeSurfer version 8.0 (beta version) on my Mac Book Pro. But somehow I am struggling to resolve the following issue when I try to open FreeView. When I checked the FreeSurfer directory - I can see that /Applic