[Freesurfer] problem with using freeview to load flattened patches

tline=1:overlay=/sig.nii.gz:overlay_threshold=2,4 -viewport 3d -zoom 1.2 -cam Elevation 90 Regards, Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://mesovision.martinos.org/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] mris_flatten Version 6 vs. 7

External Email - Use Caution Correct Luis. But I am not sure why did verion 7 act like this. Shahin Nasr, Ph. D. Assistant Professor in Radiology Harvard Medical School https://secure-web.cisco.com/1dieRkuIGIwcoRKWXF1_E_U5H9RTe

Re: [Freesurfer] mris_flatten Version 6 vs. 7

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD Sent: Friday, April 7, 2023 5:11:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7 External Email - Use Caution Hi Shahin What is your command line? mris_flatten does

Re: [Freesurfer] mris_pmake error - freadFloat: fread failed

or freeview -f On 11/12/2020 9:52 AM, Nasr, Shahin,Ph.D. wrote: Hi Surfers, For one subject, when I run mris_pmake as below: mris_pmake --subject --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:,vertexEnd: --mpmOverlay euclidean I get the following error: mris_pmake

[Freesurfer] mris_pmake error - freadFloat: fread failed

irrespective of the Start/End vertex, as far as I see. I guess this error is because a file in the subject's brain recon is corrupted. But unfortunately, the error message is not helpful. I even tried to open the error.log. But I do not see any further info there. Any suggestions? S

[Freesurfer] preproc-sess - motion correction problem

Hi Surfers, I have faced an issue with preproc-sess and I appreciate your help. I have a single slice EPI scan (number of TRs > 500; TR=0.2). When I tried to do preproc-sess, mc-afni2 is called and it crashed. When I checked the log, I noticed this: 3dvolreg.afni -verbose -dfile 005/fmc

Re: [Freesurfer] tksurfer - failed to calloc

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nasr, Shahin,Ph.D. Sent: Wednesday, July 22, 2020 12:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer - failed to calloc Hi Surfers, I get the following error when I use tksurfer for one of our subjects

[Freesurfer] tksurfer - failed to calloc

Hi Surfers, I get the following error when I use tksurfer for one of our subjects: znzTAGskip: tag=1830834290, failed to calloc 1834378240 bytes! To clarify, this error is only limited to freesurfer version 6.0 and 7. But version 5.3 works fine with the same subject. Regards __

Re: [Freesurfer] rtview - loading a tcl file

: Friday, July 17, 2020 1:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rtview - loading a tcl file OK, try again:) On 7/17/2020 1:42 PM, Nasr, Shahin,Ph.D. wrote: the tksurfer look correct as below tksurfer SUBJ lh inflated -aparc -tcl /usr/local/freesurfer/dev/lib/tcl

Re: [Freesurfer] rtview - loading a tcl file

: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Friday, July 17, 2020 1:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rtview - loading a tcl file sorry, they again On 7/17/2020 1:27 PM, Nasr, Shahin,Ph.D. wrote: tksurfer SUBJ lh inflated -aparc -tcl

Re: [Freesurfer] rtview - loading a tcl file

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rtview - loading a tcl file What is the tksurfer command that is output? On 7/17/2020 1:13 PM, Nasr, Shahin,Ph.D. wrote: Unfortunately it is not working. My command is like this: rtview --s SUBJ --real real.nii --imag imag.nii --eccen --hemi lh --fsig

Re: [Freesurfer] rtview - loading a tcl file

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Friday, July 17, 2020 1:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rtview - loading a tcl file ok, try now On 7/17/2020 12:49 PM, Nasr, Shahin,Ph.D. wrote: Thanks. But as far as I

Re: [Freesurfer] rtview - loading a tcl file

s N. Greve Sent: Friday, July 17, 2020 12:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] rtview - loading a tcl file I just added --tcl to rtview. The new version is in dev On 7/17/2020 12:23 PM, Nasr, Shahin,Ph.D. wrote: Hi Surfers, I was wondering if there is a way to load

[Freesurfer] rtview - loading a tcl file

Hi Surfers, I was wondering if there is a way to load a tcl file with rtview command. Specifically, I need to change the color table to RYGB, remove the aparc, ... . Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr

[Freesurfer] mri_vol2surf

Hi Surfers, Is there anyway to pass the full address of a surface to mri_vol2surf? To clarify, we are using surfaces that are saved outside /surf/ and we prefer not to relocate them every time that we want to use mri_vol2surf. Thanks ___ Freesurfer

[Freesurfer] freeview and complex values

Hi Surfers, I am trying to use freeview to present retinotopy mapping in subcortical regions. I need to show complex (real and imag) values generated by a retinotopy analysis in a 'color wheel' format (similar to what tksurfer does). Any hint? ___

Re: [Freesurfer] mris_fwhm problem

t;> (niters=0). When I use the same command with fwhm =1, then i see the >> difference and niters=1. >> >> My question is, why is fwhm = 0.66 not acceptable? How can i solve this >> issue. >> >> Regards >> >> _ &g

[Freesurfer] mris_fwhm problem

=1, then i see the difference and niters=1. My question is, why is fwhm = 0.66 not acceptable? How can i solve this issue. Regards _ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street

Re: [Freesurfer] fcseed-config

Your problem solved? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-

Re: [Freesurfer] fcseed-config

Massachusetts General Hospital > > 149 13th Street, 149-2615 > > Charlestown, MA, USA, 02129 > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] fmri_readreg

d lta files. If no, would >> you tell me how to extract regmat from this lta file. >> >> regards >> _ >> >> Shahin Nasr >> >> Assistant Prof. in Radiolo

[Freesurfer] fmri_readreg

updated version of fmri_readreg.m to read lta files. If no, would you tell me how to extract regmat from this lta file. regards _ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown

[Freesurfer] Contrast to Noise Ratio - mri_glmfit vs. selxavg3-sess

the same as cnr.nii generated by selxavg3-sess for the same subject. Regards _ Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School Bldg 149, 13th street, Charlestown, MA 02129

[Freesurfer] Overlap between Yeo networks and aparc2009 segments

Dear Experts, We are looking for a way to measure the amount of overlap between each 'aparc 2009 segment' vs. 'Yeo 7 networks segments'. Currently I can do that by converting segments to labels and and then measuring the number of common vertices between them. But I was wondering if there is a m

Re: [Freesurfer] upsampling ?h.curv

Hi Bruce, Would you be more specific. The command that you suggested generates ?h.white.K and ?h.white.H. I am trying to generate ?h.curv. > try running > > mris_curvature -w ... > On Wed, 30 Aug 2017, > sha...@nmr.mgh.harvard.edu wrote: > >> Dear Freesurfers, >>I want to project a map o

[Freesurfer] upsampling ?h.curv

Dear Freesurfers, I want to project a map on up-sampled inflated brain. Up-sampled inflated brain has been generated using mris_mesh_subdivide command (without any problem). But when I apply the same command to ?h.cuv I get an error message that: ERROR: MRISread: file 'surf/rh.curv' has many

Re: [Freesurfer] $SUBJECTS_DIR

Hi Adil, My understanding is that, you can always change the location of SUBJECTS_DIR. Just use this command: setenv SUBJECTS_DIR You do not need to mention this new address in your recon-all command. Good luck > HI,1-I'm working with FreeSurfer that is on a server.  I don't have > per

[Freesurfer] variable TR

Hi Surfers We are wondering if we can use freesurfer to analyze ECG-gated fmri. As far as I see, mkanalysis-sess expects a fix TR. Since we are in the design stage, any hint or suggestion to facilitate future data analysis will be highly appreciated. Regards

[Freesurfer] citation for mris_pmake

Dear Surfer, I want to cite the methods used in mris_pmake command but I can't find it in wikisurfer or the help of this command. Is the method used in this command described in a published paper? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Ha

Re: [Freesurfer] isxconcat-sess

Hi Surfers and Doug, I was trying to average two scan sessions of the same subject and isxconcat-sess under dev-env failed again. This time I get this message: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2

[Freesurfer] Freesurfer next version

Hi Freesurfer developers, As far as I see, pRF (population receptive field) mapping is not a part of current freesurfer (please correct me if I am wrong). I was wondering if you have any plan to add it to the next/upcoming freesurfer version? Regards -- Shahin Nasr PhD in Cognitive

[Freesurfer] mris_pmake Error

ards P.S.: The command that I use it like this: mris_pmake --subject --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:,vertexEnd: --mpmOverlay euclidean -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard

Re: [Freesurfer] isxconcat-sess

Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve wrote: > I just made a fix. Can you try it out and let me know if it works? > > On 05/14/2015 11:38 AM, SHAHIN NASR wrote: > > Hi, > >Does anyone know what has chan

[Freesurfer] isxconcat-sess

/cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] binary noise regressor

y, you can set up a time point >>> exclude file to exclude those time points. If you use this, then create >>> the file by putting the time in seconds of the time points you want to >>> exclude. >>> doug >>> >>> On 5/1/15 11:45 AM, SHAHIN NASR wrote

[Freesurfer] binary noise regressor

I need to do for the regressor! A sample regressor file is attached. It has 98 rows corresponding to 98 TRs that we have in the experiment! Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ShockNUI_Fin Description: Binary data

[Freesurfer] Measuring the distance relative to a path

Hi Surfers, I need to measure the ''minimum' distance between a cortical vertex and a manually defined path (e.g. V2-V3 border). Is there any command or straightforward way to do that? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard

Re: [Freesurfer] -per-run analysis in native space

/mri_fwhm --mask /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz --i /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz --o /autofs/cluster/tootell/pitcairn/1/shahin

[Freesurfer] -per-run analysis in native space

right? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

[Freesurfer] registration problem

Hi, For one of my subjects, I have noticed a misalignment between sig.nii and orig.mgz when I try to show the sig map using either tkmedit (as below): cd /autofs/cluster/tootell/pitcairn/1/shahin/V2_Ori/Analysis tkmedit-sess -s ../Subjects/auil2 -a OriExp_TR3_1p5mm_PR -c ANG_90_45 or

Re: [Freesurfer] FIR analysis on regions of interest...

__ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.har

Re: [Freesurfer] bbregister for MRA

then transfer that > registration to the partial FoV assuming that the whole and partial share a > scanner space (which they will if acquired at the same time). The > intermediate can be anything, eg, fMRI, anatomical, B0 map, low-b DTI > volume. > > doug > > >

Re: [Freesurfer] bbregister for MRA

version of our MRA and how good it was when we used T1+pial registeration: tkregister2 --mov /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010/001_nu.nii --reg /cluster/tootell/pitcairn/1/shahin/ColorPrj/MRA_Study/Sbj/auil_2/MRA_500_pre_contrast/010

Re: [Freesurfer] fieldsign map display

r/local/freesurfer/lib/tcl/fsgdfPlot.tcl > Reading /usr/local/freesurfer/tktools/tkUtils.tcl > Successfully parsed tksurfer.tcl > reading white matter vertex locations... > % ^CKilled > Area degli allegati > Visualizza anteprima allegato fieldsign_map.tiff > Fai clic qui per rispondere

[Freesurfer] Average myelination within ROI

.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar

[Freesurfer] bbregister for MRA

increases the registration time. Regards P.S.: using --t2 in bbregister (instead of --bold) generated the same outcome but --t1 was completely off. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

[Freesurfer] mri_segstats

Hi, I have two questions about mri_segstats. I want to measure the surface area of a functionally-defined ROI. I used the mri_segstats as below and I want to be sure that it is correct. Please note that ROIs were defined in the native space. mri_segstats --i $SUBJECTS_DIR/SBJ1/surf/rh.area -

[Freesurfer] mc-bbr

-- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

Re: [Freesurfer] selxavg3-sess error

Hopefully this is the last problem with per-run analysis (in native space) but as far as I see, preproc-sess and selxavg3-sess do not generate /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/register.dof6.dat Because of that, when I use tksurfer-sess it faces an error

Re: [Freesurfer] selxavg3-sess error

gt;>> -per-run >>>> >>>> >>>> But using -mcprextreg flag generates an error. Is it a bug? >>>> >>>> >>>>> There is not an mcextreg file there. There is mcprextreg file. I >>>>> think >>>>&g

Re: [Freesurfer] selxavg3-sess error

there. There is mcprextreg file. I think >>> you need to run preproc with -per-session to get the mcextreg file >>> doug >>> >>> On 03/18/2014 02:34 PM, SHAHIN NASR wrote: >>>> Hi, >>>> When I run selxavg3-sess, I face this error: >>

Re: [Freesurfer] selxavg3-sess error

gt;>> native >>>>>> space). I assumed that I have to change my mkanalysis-sess to this: >>>>>> >>>>>> mkanalysis-sess -analysis ColorPrj_TR4_1p5mm_PR_ANOVA -fwhm 1.5 >>>>>> -paradigm >>>>&

Re: [Freesurfer] selxavg3-sess error]

nditions 8 -refeventdur 14 -force -fsd bold_Color -per-run But using -mcprextreg flag generates an error. Is it a bug? > > There is not an mcextreg file there. There is mcprextreg file. I think > you need to run preproc with -per-session to get the mcextreg file > doug > > On

[Freesurfer] selxavg3-sess error

Hi, When I run selxavg3-sess, I face this error: ERROR: cannot find volume matching /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg ERROR: loading nonpar reg /autofs/cluster/tootell/pitcairn/1/shahin/ColorPrj/7T/Sbj/myla2/bold_Color/013/mcextreg

[Freesurfer] per-run and Native space

run selxavg3-sess, it returns an error that > cannot determine format of > test/bold/013/fmcpr.sm1.5 and exits. Would you tell me why those files are not generated? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical

[Freesurfer] absolute value of effect size

Hi, I have two related questions. I have two conditions (e.g. C1 and C2) and I want to generate a map that shows all voxels that can differentiate C1 from C2 *irrespective* of whether C1>C2 or C1___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] saving in GIFTI .func.gii format

Hi Surfers I have done a surface-based group-averaged mapping and now I need to save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii format. Does mri_glmfit support this output format? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH

[Freesurfer] using multiple functional ROIs in fcseed-config

manually average the .dat files? Should we consider anything in this averaging? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Why don't no-mask flag work?

RetinaPrj_New I am also attaching the analysis.info If you want to test the files, you can see the subject files in: /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir Note: I did all of these tests from scratch after deleting files from the previous tests. So it can't be due to a rema

Re: [Freesurfer] Why don't no-mask flag work?

; > On 10/03/2013 10:29 AM, SHAHIN NASR wrote: >> Hi Doug, >> Did you have a chance to find the reason for this problem? >> >> >> On Wed, Oct 2, 2013 at 3:20 PM, > <mailto:sha...@nmr.mgh.harvard.edu>> wrote: >> >> I still re

Re: [Freesurfer] Why don't no-mask flag work?

I still receive the same error message (1mm is now 2mm in the message). outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask2 Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53

[Freesurfer] Why don't no-mask flag work?

-gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd bold -no-mask I get this error: outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask Error using MRIread (line 76) ERROR: cannot determine

[Freesurfer] cvs_avg35

Hi, Would you tell me where I can find cvs_avg35 brain template. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

a model as we do for spmhrf or fslhrf, but just for the negative >> peak? >> >> Regards >> >> That's the problem Doug. I have already generated the FIR model but how >>> can >>> I show the sig MAP for one "particulat time point". Wha

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

f, but just for the negative >> peak? >> >> Regards >> >> That's the problem Doug. I have already generated the FIR model but how >>> can >>> I show the sig MAP for one "particulat time point". What are the other >>>

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

int". What are the other > ways? > > > On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve > wrote: > >> Hi Shahin, there are several ways that you could do it. The one that >> immediately comes to mind is to use an FIR and then test for a >> dif

[Freesurfer] Fwd: Comparing HRF undershoots between conditions

That's the problem Doug. I have already generated the FIR model but how can I show the sig MAP for one "particulat time point". What are the other ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve wrote: > Hi Shahin, there are several ways that you could do it. The one

[Freesurfer] Comparing HRF undershoots between conditions

Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions independent from the positive peak. Is there anyway, to generate this map? P.S.: Please note that I need a map and not a time course graph. -- Shahin

[Freesurfer] selxavg3-sess problem with -per-run flag

2.25 1.25 -mcextreg -TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force This time when I ran selxavg3-sess command I faced this error: ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5 (MRIread) Error in flac

Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans

fMRI, but it could also be > an anatomical if you wanted to collect that. > doug > > > On 02/25/2013 02:39 PM, SHAHIN NASR wrote: >> Hi, >> We are planning to collect high resolution _functional_ MRI for a >> group of subjects with voxel size smaller than 1 mm. For the

[Freesurfer] High resolution fMRI and resolution of anatomical scans

mapping fMRI data to fsaverage space. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

Re: [Freesurfer] task-related functional connectivity analyses freesurfer 5.1.0

ly. On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve wrote: > Hi Shahin, you can do seed-based analysis. In principle you can do this > with task data, you just need to adjust your conclusions accordingly. There > is no easy to way to only do the analysis on the resting epochs of a &

[Freesurfer] task-related functional connectivity analyses freesurfer 5.1.0

been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurf

[Freesurfer] Non rigid registration

possibility or not. If yes, then I appreciate if you can introduce me a reference (published article) to support our answer. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list

Re: [Freesurfer] Recent paper on FreeSurfer reliability

; > Cheers, > Ed > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Ce

[Freesurfer] averaging sessions with different TRs

Hi, I was wondering if I can average two scan sessions with different TRs or not. Number of conditions and all other factors are exactly the same between the two sessions. regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://ma

[Freesurfer] Per-run registration in monkey fmri

Hi In monkey fmri, we usually have to do the functional-anatomical registration manually since bbregister doesn't work very well. It was easy in version 4.5 since we usually used just one run for registration. In version 5.1 we can use per-run option to improve registration but I am wonderi

[Freesurfer] Selxavg3-sess Out of Memory - What are the options?

it is not possible in version 5. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Event-Related design and jitter in stimulus onset

) Also, for "psdmin psdmax" I wasn't sure if they are number of TRs or number of seconds and what is a safe window length when my stimuli are very simple visual objects (and no cognitive task). Once again, thanks for your help. On Fri, Dec 9, 2011 at 1:10 PM, Douglas N Greve wrot

[Freesurfer] Event-Related design and jitter in stimulus onset

Hi Surfers, It is my first experience with Event-related paradigms. In my experiment, trials take minimum 6s (TR=2s). I wonder what is the optimum variable delay between trials to be able to analyze data without any confound. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos

Re: [Freesurfer] problem with generating cesvar.nii

sum of the dofs of the individual subjects. Why > are you using a fixed-effects model? > doug > > SHAHIN NASR wrote: > >> Thanks Doug. Just one related question. Should I also generate a new >> ffxdof.dat file for this map? I assumed that ffxdof depends on the number o

Re: [Freesurfer] problem with generating cesvar.nii

-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve wrote: > Hi Shahin, it is not as simple as doing a subtraction of the cesvar files. > What you are trying to get is the expected variance of your difference > between the ces files (as a variance, i

[Freesurfer] problem with generating cesvar.nii

or in rh.cesvar.nii file (am I right?). Would you tell me how can I fix this problem? P.S.: please note that sequence of subjects and all MRI parameters are exactly the same between the two maps. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Har

[Freesurfer] funcroi-table-sess with multiple contrasts

Hi, Is there anyway to print multiple contrasts in one output file using funcroi-table-sess command? -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer

[Freesurfer] using isxconcat for partial correlation coefficient map

Hi, Would you tell me how can I use isxconcat-sess to calculate group averaged "partial correlation coefficient map"? I have already generated pcc.nii files for each individual subject. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medi

[Freesurfer] Partial brain scanning and registeration

Hi I want to know if there is any limit for the automatic registration of functional scans on structural ones when we are scanning activity just in a specific part of the brain (e.g. occipital cortex). ___ Freesurfer mailing list Freesurfer@nmr.mgh

[Freesurfer] Problem with fcseed-config and fcseed-sess

Hi, I have faced a problem using ROI-based, fcseed-config and fcseed-sess I used either: fcseed-config -roi /cluster/tootell/pitcairn/1/shahin/good_subjects_anat/atou_anat/label/rh.V1.label -fcname mean.R_V1.dat -fsd bold -mean -cfg mean.R_V1.config OR: fcseed-config -roi /cluster/tootell

[Freesurfer] Error in generating V1 labels

nat/label/rh.v1.predict.label Would you tell me what is the possible error/problem? P.S.: I used both ver 4.5 and 5.0 and the result was the same. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Fre

Re: [Freesurfer] how to generate aparc.annotion files?

Ok now I faced another problem saying that I dont have talairach.xfm for monkeys. Would you tell me how can I generate it for monkeys?  Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Douglas N Greve To

Re: [Freesurfer] how to generate aparc.annotion files?

saying that I don't have a lh and rh.aparc.annot files.     Apparently very old versions of freesurfer (version 3) didnt need these files. Am I right? Do you suggest to use old versions?  Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical S

Re: [Freesurfer] how to generate aparc.annotion files?

Thanks Bruce,    To avoid this problem, is there anyway to run make_average_subject without having lh and rh.aparc.annot files?  Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School From: Bruce Fischl To: Shahin

[Freesurfer] how to generate aparc.annotion files?

Hi Freesurfers,    Anybody knows how can I make lh and rh.annotation.aparc files for a monkey? I need them initiate an brain averaging process. Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

[Freesurfer] func2roi and register.dat in version 5.0

Hi,     In version 5.0 "register.dat" file is not generated. I was wondering if I should instead use "register.dof6.dat" in fun2roi or something else. Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Ha

[Freesurfer] fwhm vs. fwhm-surf in version 5.0

t do smoothing on the basis of volume or surface and how significant the difference is? Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesu

[Freesurfer] Error in selxavg3-sess with -sf option

"Analysis.rh" folder in the session folders.   When I applied the same command to each indivisual session by: "selxavg3-sess -s Session1 -a Analysis.rh", it works perfectly and generates the Analysis.rh folder.   Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos

[Freesurfer] activity time course

Hi, Would you tell me how can I see time-course of activities within one ROI (averaged over voxels) for each experiment condition? Should I use matlab commands?  Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

[Freesurfer] Comparing results of independent experiments

Hi Doug and freesurfers, My subjects have participated in two independent experiments within two different sessions (e.g. experiment 1 in day 1 and experiment 2 in day 2). Now I want to see if the contrast between conditions of experiment 1 and 2 is significant or not. For instance I want

[Freesurfer] How can I make aparc.2009 from aparc.2005

Hi everyone    For my old subjects I already have aparc.2005 atlas file in the label directory but not the 2009a version. I want to know how can I make 2009 version for these subjects without doing the recon-all for them.  Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center

[Freesurfer] How to compare conditions scanned within different runs?

    I want to compare 2 different experimental conditions that were scanned within different runs. For example assume that, in ten runs I have had conditions 1 and 2 and in another ten runs I have had condition 3 and 4. Now I want to compare condition 1 and 3. Is it possible?  Regards Shahin