Re: [Freesurfer] comparing left and right cortical thickness

> Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not

Re: [Freesurfer] bbregister and fnirt

rang > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos C

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

___ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358

Re: [Freesurfer] A newbie to fMRI analysis

imaging department > Department of Psychiatry > 451, biomedical research building > University at Buffalo (south campus) > Buffalo, NY-14216 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu

Re: [Freesurfer] A newbie to fMRI analysis

y by providing the correct path. Or drag/drop into the window if you are using the gui. > > Thanks and regards, > > Sampada > > > > On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh < > shant...@nmr.mgh.harvard.edu> wrote: > >> You can convert Dicom using MR

Re: [Freesurfer] A newbie to fMRI analysis

You could also try the nipy version. works real well with Snow Leopard OS shantanu On Mon, April 28, 2014 9:09 pm, Shantanu Ghosh wrote: > Hi Sampada, > > Please cc the freesurfer list when answering/asking questions so others > can answer too. And also people with similar issues

[Freesurfer] basic segmentation stats question

Dear Freesurfers, Pardon me for a very basic question. If I wanted to extract the hemisphere-wise GM and WM values for multiple subjects using a single command, what is the best way to do it? Thanks in advance. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts Gen

Re: [Freesurfer] A newbie to fMRI analysis

724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoi

Re: [Freesurfer] A newbie to fMRI analysis

nvert all the eight files at one > go. > > mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > '/Users/sampada/Desktop/test/mri/org/.mgz' > > > Regards, > > Sampada > > > On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh > > wrot

Re: [Freesurfer] A newbie to fMRI analysis

sorry try: cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.mgz Hth, shantanu On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: > You don't need the quotation marks in your path > also, it seem

Re: [Freesurfer] A newbie to fMRI analysis

ne time for all .mgz file(which are eight in numbers)? And what > command do I use for recon-all? I have tried many but none is working.. > > Thanks and regards, > > Sampada > > > > > > > On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < > shant...@nmr.mgh

Re: [Freesurfer] mgz to dicom

h.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurf

Re: [Freesurfer] Transform SMOOTHWM to DTI B0

ttp://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. >> >> > ___ >

Re: [Freesurfer] Template from scratch

gt;> Sophie >>>> >>>> >>> >>> >>> 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 >>&

Re: [Freesurfer] Merging the labels to T1 image

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 wa

Re: [Freesurfer] adding grey matter

>>>> or something like that? >>>> Thanks for your help. >>>> Claudia >>>> >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it >>> is >>> add

Re: [Freesurfer] Make an average activation map of 2 scans

elxavg3-sess referencing the pre and post bold runs in the runlist > file? Any clarification or suggestions would be greatly appreciated! > > Thanks, > Alex > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] (no subject)

Hello Freesurfer experts, How can I specify multiple contrasts for my thickness study with two groups AA and BB, having different number of subjects in each group? My variables are tract-wise FA values, age and IQ. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for

[Freesurfer] specifying multiple contrasts

Hello Freesurfer experts, How can I specify multiple contrasts for my thickness study with two groups AA and BB, having different number of subjects in each group? My variables are tract-wise FA values, age and IQ. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for

[Freesurfer] vertex-by-vertex thickness

vance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] vertex-by-vertex thickness

div std.mgh -o z.mgh > Visualize > tksurfer fsaverage lh inflated -overlay z.mgh > > > > > On 06/13/2012 11:26 AM, Shantanu Ghosh wrote: >> Hi FS experts, >> >> Sorry if this is a newbie question. >> >> I want to display how an individual patient's crti

Re: [Freesurfer] vertex-by-vertex thickness

n 06/13/2012 04:38 PM, Shantanu Ghosh wrote: >> hi doug, >> i notice slight differences in numbers when using fscalc vs. fscalc.fsl >> for calculating the z-score map\ I am just curious why it may happen >> thanks in advance, >> shantanu >> >> >> >

[Freesurfer] mri_register memory error

1340 labels @ (0,0,0) Cannot allocate memory Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology ___ Freesurfer mailing list Freesurfer@n

Re: [Freesurfer] mri_register memory error

er? I don't ink mri_register is what you > want. Possibly mris_register instead (note the "s")? > Cheers > Bruce > > > > > On Jun 15, 2012, at 8:32 PM, "Shantanu Ghosh" > wrote: > >> >> Hi Freesurfer experts, >> >&

Re: [Freesurfer] error loading datatable in qdec

__ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging _

Re: [Freesurfer] error loading datatable in qdec

vels is > invalid. Must have at least two levels. > Error loading the data table. > > although there are two levels in the .levels filehow is that possible? > > 2012/11/19 pietro de rossi > >> thanks...I'll try... and let you know... >> >> >>

[Freesurfer] Registering individual subjects to MNI152

in 3a) with the warpfield from the registration form step 2) above. Or is there something I am missing here? Also, for 3a) how do I get the correct set of triangles for each vertex? Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital

[Freesurfer] Reposting: Registering individual subjects to MNI152 and other questions

Dear Freesurfers, I posted the questions yesterday but received no answer so far. I really need help with this. Posting thsi again. Thanks in advance, and sorry for the double posting. S On Sat, January 12, 2013 2:02 pm, Shantanu Ghosh wrote: > Dear freesurfer experts, > > I have .si

[Freesurfer] Error with mri_vol2surf

, -1): could not open file ERROR: could not read /volstat/AC066-rh-volume.mgh as type 3 Thanks for all the help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Ima

[Freesurfer] [Fwd: Re: Error with mri_vol2surf]

Original Message Subject: Re: [Freesurfer] Error with mri_vol2surf From:"Shantanu Ghosh" Date:Wed, January 16, 2013 2:05 pm To: "

[Freesurfer] Citation for mri_glmfit-sim

Hi Freesurfers, Can you point out the correct paper that I can cite for the clusterwise correction for multiple comparisons computed by mri_glmfit-sim in v5.0 ? Thanks, Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomed

Re: [Freesurfer] R: Re: R: Re: tracula and recon-all

il 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

Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: tracula and recon-all

ve a freesurfer recon of your subject's T1 in the >> >> > >> $SUBJECTS_DIR? >> >> > >> >> >> > >> On Sun, 3 Feb 2013, std...@virgilio.it wrote: >> >> > >> >> >> > >> > I think that I h

Re: [Freesurfer] creating 'Mid' surfaces

edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

Re: [Freesurfer] creating 'Mid' surfaces

sorry the files are in the surf directory On Thu, February 14, 2013 9:53 am, Shantanu Ghosh wrote: > Hi Christine, > If you cd to the subject directory you can locate the ?h.white surface and > use mris_expand command to do this. > Hth, > Shantanu > > On Thu, February 14

[Freesurfer] Surface area computation

Hello FreeSurfer experts, Has algorithm described in Winkler et al. (2012) Neuroimage paper for computation of surface area been incorporated in v5.1, or is it part of the 5.2b implementation? Thanks for your help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachus

Re: [Freesurfer] Surface area computation

+ that could run faster > than the Matlab version, let me know and I'd be happy to help! > > All the best, > > Anderson > > > 2013/2/15 Shantanu Ghosh > >> Hello FreeSurfer experts, >> >> Has algorithm described in Winkler et al. (2012) Neuroimage pape

Re: [Freesurfer] nb0 question

etts 2129 > U.S.A. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General

Re: [Freesurfer] dual installation question

harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] dual installation question

Or you may have multiple freesurfer versions within the freesurfer director, something like /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc. and then export FREESURFER_HOME=/freesurfer/5.1 etc Hth, S. On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote: > Hi J

Re: [Freesurfer] mris_preproc --meas thickness

, > how can I do? > Thanks, > > Stefano > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School & Ma

Re: [Freesurfer] mris_preproc question

d. 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 inform

Re: [Freesurfer] Error

ighthippocampus 4006 > Error loading the data table. > > Many Thanks > chikku > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, P

Re: [Freesurfer] Error

atomy.levels is invalid. Must > have at least two levels. > Error loading the data table. > > > Kind Regards > chikku > > > > > > > > > > On 6 March 2013 18:19, Shantanu Ghosh > wrote: > >> ok try editing qdec.table.dat by just pressing after

Re: [Freesurfer] multi-echo mprage

souheil.in...@nih.gov >> 301-402-9409 >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >

Re: [Freesurfer] A newbie to fMRI analysis

aibhav2 sampada$ recon-all -s s600a1001.mgz '-all' > > ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz > > > Even when I make the intermediate directory of mri/orig, its still not > recognising the command and shows an error. > > > Thanks and rega

Re: [Freesurfer] A newbie to fMRI analysis

ory. > > Will you please let me know where I am going wrong? > > Thanks and regards, > > Sampada > > > On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh < > shant...@nmr.mgh.harvard.edu> wrote: > >> You should set your SUBJECTS_DIR variable to the directory

Re: [Freesurfer] A newbie to fMRI analysis

e an > intermediate directory for the recon all process to run? > > Thanks and regards, > > Sampada > > > On Thu, May 15, 2014 at 5:23 PM, Shantanu Ghosh < > shant...@nmr.mgh.harvard.edu> wrote: > >> remove the quotation marks from '-all' and try again &g

[Freesurfer] TRACULA: ERROR in -qa Flag

antanu[121] trac-all -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt ERROR: flag -qa unrecognized -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt glia:shantanu[122] Thanks in advance for all help. Shantanu -- Shantanu Ghosh, Ph.

[Freesurfer] TRACULA: Exits with Errors, and ERROR in -qa Flag

not recognize the -qa flag. What am I doing wrong? Attached is the log file, and an updated config file. Any help is highly appreciated. Thanks. Shantanu Original Message Subject: TRACULA: ERROR in -qa Flag From:"Shantanu

Re: [Freesurfer] TRACULA: ERROR in -qa Flag

thanks. On Fri, June 13, 2014 12:30 pm, Anastasia Yendiki wrote: > > The right one to source is /usr/local/freesurfer/nmr-dev-env > > > On Fri, 13 Jun 2014, Shantanu Ghosh wrote: > >> Hi Anastasia, >> >> Thanks for the reply. >> >> After I edit m

Re: [Freesurfer] TRACULA: ERROR in -qa Flag

which case you don't need to download anything. > > a.y > > On Mon, 2 Jun 2014, Shantanu Ghosh wrote: > >> Dear Anastasia and Freesurfer experts, >> I am trying to set up an analysis of motion parameters using the flag -q >> from a set of DTI Dicoms located

Re: [Freesurfer] Vertex-wise comparison thickness left and right hemisphere

ed test to perform such a comparison? > > Best, > Martijn > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical Sc

Re: [Freesurfer] Tracula -qa flag

ld have gone wrong? Do I have to download the updated > Tracula version from here: http://ftp.nmr.mgh.harvard.edu/fswiki/Tracula ? > > Thank you, > Trang > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail

[Freesurfer] Making Substancia Nigra label

vance. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg ___ Freesurfe

[Freesurfer] DTImap

Hi FS experts, Is the DtiMap software (www.kennedykrieger.org) compatible with Freesurfer/Tracula? Thanks Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, i

Re: [Freesurfer] DTImap

the other software into tracula or vice versa? > > a.y > > On Mon, 21 Jul 2014, Shantanu Ghosh wrote: > >> Hi FS experts, >> >> Is the DtiMap software (www.kennedykrieger.org) compatible with >> Freesurfer/Tracula? >> >> Thanks >> Shantanu >

[Freesurfer] trac-all -prep problem

INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we

Re: [Freesurfer] unpacksdcmdir

npack the non Siemens DICOMs? > > Thanks, > Moahmad > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shantanu Ghosh, Ph.D. Harvard Medical School &a

[Freesurfer] Failure to download

Hi freesurfers, I tried to download the tutorial dataset for inspection of fs output, but receive this error message repeatedly, even with the -c flag: glia:shantanu[30] wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz --2012-04-20 15:27:05-- ftp://surfer.nmr.