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

2013-04-10 Thread shahin
ways? On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: 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 difference at a particular post stimulus time point. doug On 04

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

2013-10-02 Thread shahin
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

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

2013-10-03 Thread shahin
? 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, sha...@nmr.mgh.harvard.edu mailto:sha...@nmr.mgh.harvard.edu wrote: I still receive the same error message (1mm is now 2mm in the message

Re: [Freesurfer] selxavg3-sess error]

2014-03-19 Thread shahin
02:34 PM, SHAHIN NASR wrote: 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

Re: [Freesurfer] selxavg3-sess error

2014-03-19 Thread shahin
-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 03/18/2014 02:34 PM, SHAHIN NASR wrote: Hi

Re: [Freesurfer] selxavg3-sess error

2014-03-19 Thread shahin
-nconditions 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 03/18/2014 02:34 PM, SHAHIN

Re: [Freesurfer] selxavg3-sess error

2014-03-19 Thread shahin
? 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 03/18/2014 02:34 PM, SHAHIN NASR wrote: Hi, When I run selxavg3-sess, I face this error: ERROR: cannot find volume matching /autofs/cluster/tootell

[Freesurfer] mri_segstats

2014-06-09 Thread shahin
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

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

2013-02-25 Thread shahin
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 these subjects, we already have reconstructed _anatomical _scans with 1 mm voxel size

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

2010-03-12 Thread Shahin
    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

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

2010-07-02 Thread Shahin
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] Comparing results of independent experiments

2010-07-31 Thread Shahin
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

[Freesurfer] activity time course

2010-08-12 Thread Shahin
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] fwhm vs. fwhm-surf in version 5.0

2010-08-22 Thread Shahin
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] how to generate aparc.annotion files?

2010-11-08 Thread Shahin
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

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

2010-11-08 Thread Shahin
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 fis

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

2010-11-08 Thread Shahin
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 School

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

2010-11-08 Thread Shahin
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 gr

[Freesurfer] Error in generating V1 labels

2011-06-02 Thread Shahin
.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 ___ Freesurfer mailing

[Freesurfer] variable TR

2015-12-22 Thread shahin
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

Re: [Freesurfer] $SUBJECTS_DIR

2016-08-20 Thread shahin
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 >

Re: [Freesurfer] upsampling ?h.curv

2017-08-30 Thread shahin
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

[Freesurfer] upsampling ?h.curv

2017-08-30 Thread shahin
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

[Freesurfer] Overlap between Yeo networks and aparc2009 segments

2017-10-11 Thread shahin
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

Re: [Freesurfer] fmri_readreg

2018-02-09 Thread shahin
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

2018-02-09 Thread shahin
if there is an 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

2017-12-21 Thread shahin
it is not 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

Re: [Freesurfer] fcseed-config

2018-07-31 Thread shahin
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

Re: [Freesurfer] fcseed-config

2018-07-26 Thread shahin
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

[Freesurfer] Comparing HRF undershoots between conditions

2013-04-10 Thread SHAHIN NASR
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] Fwd: Comparing HRF undershoots between conditions

2013-04-10 Thread SHAHIN NASR
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 gr...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways that you could do

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

2013-04-11 Thread SHAHIN NASR
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 gr...@nmr.mgh.harvard.edu**wrote: Hi Shahin, there are several ways that you could do it. The one that immediately comes

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

2013-04-24 Thread SHAHIN NASR
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 gr...@nmr.mgh.harvard.edu**wrote: Hi Shahin, there are several ways that you could do

[Freesurfer] cvs_avg35

2013-07-28 Thread SHAHIN NASR
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

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

2013-10-02 Thread SHAHIN NASR
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 format

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

2013-10-03 Thread SHAHIN NASR
-a 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 remaining

[Freesurfer] using multiple functional ROIs in fcseed-config

2013-10-10 Thread SHAHIN NASR
to 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

[Freesurfer] saving in GIFTI .func.gii format

2013-11-08 Thread SHAHIN NASR
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] absolute value of effect size

2014-01-07 Thread SHAHIN NASR
, then: 1) Can I apply the same command to ces.nii file to have the absolute value of the effect size (i.e. abs(C1-C2 effect size)) or should I consider other factors? 2) Do I need to apply the same routine to cesvar? Thanks -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH

[Freesurfer] per-run and Native space

2014-03-14 Thread SHAHIN NASR
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 School

[Freesurfer] selxavg3-sess error

2014-03-18 Thread SHAHIN NASR
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

Re: [Freesurfer] selxavg3-sess error

2014-03-19 Thread SHAHIN NASR
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

[Freesurfer] mc-bbr

2014-03-27 Thread SHAHIN NASR
-- 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

[Freesurfer] averaging sessions with different TRs

2012-06-09 Thread SHAHIN NASR
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

Re: [Freesurfer] Recent paper on FreeSurfer reliability

2012-06-20 Thread SHAHIN NASR
@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Non rigid registration

2012-07-30 Thread SHAHIN NASR
this 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

[Freesurfer] task-related functional connectivity analyses freesurfer 5.1.0

2012-10-23 Thread SHAHIN NASR
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 ___ Freesurfer mailing

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

2012-10-24 Thread SHAHIN NASR
. On Wed, Oct 24, 2012 at 1:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: 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

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

2013-03-29 Thread SHAHIN NASR
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

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

2011-09-06 Thread SHAHIN NASR
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] Partial brain scanning and registeration

2011-09-20 Thread SHAHIN NASR
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] using isxconcat for partial correlation coefficient map

2011-09-26 Thread SHAHIN NASR
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 Medical School

[Freesurfer] funcroi-table-sess with multiple contrasts

2011-10-04 Thread SHAHIN NASR
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] problem with generating cesvar.nii

2011-10-19 Thread SHAHIN NASR
(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 Harvard Medical School

Re: [Freesurfer] problem with generating cesvar.nii

2011-10-19 Thread SHAHIN NASR
-sess for either map1 or map2. Right? On Wed, Oct 19, 2011 at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: 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

Re: [Freesurfer] problem with generating cesvar.nii

2011-10-19 Thread SHAHIN NASR
be roughly the 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 of subjects (session

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

2011-12-08 Thread SHAHIN NASR
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] Event-Related design and jitter in stimulus onset

2011-12-09 Thread SHAHIN NASR
...@nmr.mgh.harvard.eduwrote: Hi Shahin, there are several ways to answer this question. If you are going to analyze assuming a shape to the HRF, then the actual delay between stimuli is technically not important (though 4s will be good to avoid attenuation in the following stimulus). If you're using an FIR model

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

2012-01-11 Thread SHAHIN NASR
. -- 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

[Freesurfer] Per-run registration in monkey fmri

2012-01-20 Thread SHAHIN NASR
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

[Freesurfer] bbregister for MRA

2014-08-20 Thread SHAHIN NASR
if it 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] Average myelination within ROI

2014-09-03 Thread SHAHIN NASR
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.harvard.edu

Re: [Freesurfer] fieldsign map display

2014-09-04 Thread SHAHIN NASR
@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] bbregister for MRA

2014-09-30 Thread SHAHIN NASR
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] bbregister for MRA

2014-09-30 Thread SHAHIN NASR
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 On 09/30/2014 12:41 PM, SHAHIN NASR wrote: Hi Doug, Sorry

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

2014-10-14 Thread SHAHIN NASR
://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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

[Freesurfer] registration problem

2014-11-14 Thread SHAHIN NASR
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

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

2015-04-01 Thread SHAHIN NASR
/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

2015-03-27 Thread SHAHIN NASR
? -- 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

[Freesurfer] Measuring the distance relative to a path

2015-04-21 Thread SHAHIN NASR
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 Medical School

[Freesurfer] binary noise regressor

2015-05-01 Thread SHAHIN NASR
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

Re: [Freesurfer] binary noise regressor

2015-05-06 Thread SHAHIN NASR
in seconds of the time points you want to exclude. doug On 5/1/15 11:45 AM, SHAHIN NASR wrote: Hi Surfers I want to remove the possible effects of a binary noise (electric shock) from the evoked fMRI. To do so, I have generated a regressor file in which all TRs in which electric shock has been

[Freesurfer] isxconcat-sess

2015-05-14 Thread SHAHIN NASR
/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] isxconcat-sess

2015-05-14 Thread SHAHIN NASR
Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 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 changed

[Freesurfer] mris_pmake Error

2015-05-20 Thread SHAHIN NASR
.: The command that I use it like this: mris_pmake --subject Sbj --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:Vert1,vertexEnd:Vert2 --mpmOverlay euclidean -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

[Freesurfer] Freesurfer next version

2015-06-21 Thread SHAHIN NASR
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

Re: [Freesurfer] isxconcat-sess

2015-07-06 Thread SHAHIN NASR
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] citation for mris_pmake

2015-08-01 Thread SHAHIN NASR
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 Harvard