[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] Fwd: Comparing HRF undershoots between conditions

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 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak

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

to mind is to use an FIR and then test for a difference at a particular post stimulus time point. doug On 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak of activity) between two conditions

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

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 04/10/2013 03:54 PM, SHAHIN NASR wrote: Hi, I want to generate a map to show the significant difference between HRF undershoot (negative peak

[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

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

and -no-subcort-mask in the preproc-sess *** If I remove this flag, everything looks fine except for the fact that all activity outside brain is masked! -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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

-session and mni305-2mm but still did not help. I even tried doing it in native space (by not mentioning mni305/fsaverage) but did not work either. What was your preproc-sess command? On 10/03/2013 10:29 AM, SHAHIN NASR wrote: Hi Doug, Did you have a chance to find the reason

[Freesurfer] using multiple functional ROIs in fcseed-config

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

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

, 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

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

for this subjects (and why I don't see it for the other subjects)? 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] selxavg3-sess error

? 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

[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

[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

Re: [Freesurfer] Recent paper on FreeSurfer reliability

@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

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

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

of a blocked design, if that is what you mean. doug On 10/24/2012 12:55 AM, SHAHIN NASR wrote: Hi, I was wondering if we can compare functional connectivity between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state

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

fmcpr.sm5.self.lh.nii.gz Notably, if I drop that -per-run flag from my mkanalysis-sess then system works without any problem. But then I am not sure whether I have processed my data in per-run or per-session mode. Any help will be appreciated Regards -- Shahin Nasr PhD in Cognitive

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

for the session of interest (e.g. atou) fcseed-sess -s atou -cfg mean.R_V1.config -make-mask but I just get a if: Expression Syntax. message and the expected dat file is not generated. Do you have any idea what is wrong? Any help will be highly appreciated. -- Shahin Nasr PhD in Cognitive

[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] 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 Medical School

[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] problem with generating cesvar.nii

(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

(as a variance, it must be positive). To get this you need cesvardiff = (cesvar1+cesvar2)/(2^2) The 2^2 is the number of inputs (2) squared. doug SHAHIN NASR wrote: Hi, I have generated two different functional connectivity maps for two different ROI-based seeds. These maps are based on group

Re: [Freesurfer] problem with generating cesvar.nii

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

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

of the HRF (no assumed shape), then I usually advise that you have, in total, as much time spent on fixation (or whatever your null stimulus is) as you have for any other stimulus. You can use optseq to compute the actual schedule. doug SHAHIN NASR wrote: Hi Surfers, It is my first

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

. -- 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

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

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

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

@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

here because the GM will probably be brighter than CSF. doug On 08/20/2014 04:54 PM, SHAHIN NASR wrote: Hi Surfers I want to use bbregister to register my MRA scans to the structural scans. The first attempts by using these parameters came out OK but not perfect: bbregister --s

Re: [Freesurfer] bbregister for MRA

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...

://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

process my data in in nmr-dev-env but I have also checked the above lines in nmr-stable53-env and problem is still there. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer

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

that that will produce huge files (float images 256^3 by number of time points). doug On 03/27/2015 01:50 PM, SHAHIN NASR wrote: Hi Surfers, I want to find a way to analyze subcortical activities in native space and still take advantage of per-run registration. As far as I understand

[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 Medical School

[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

Re: [Freesurfer] binary noise regressor

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

/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

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

.: 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

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

.lh/nmask.dat Which is true! this file does not exist. Regards On Thu, May 14, 2015 at 10:39 PM, SHAHIN NASR sha...@nmr.mgh.harvard.edu wrote: 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

[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 Harvard