[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

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

e 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.

[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

[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

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] 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 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] 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

[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 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> wr

[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

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

used -nomask 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 Harvar

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

-nomask >> -no-subcort-mask >> >> I also tried per-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? &g

[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

[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

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] 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] selxavg3-sess error

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

Re: [Freesurfer] selxavg3-sess error

(in > >>>>>> 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

[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

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

5.self.rh.nii.gz 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 Cognit

[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

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 differe

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

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 >

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

t 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 FI

[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] 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

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] 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

[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

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

gt; 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 freesurfe

[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

[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] 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

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

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 para

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] 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

[Freesurfer] registration problem

S.: I 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 Frees

[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

[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] 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] 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

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

Re: [Freesurfer] problem with generating cesvar.nii

t 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

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

[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

ng an FIR model 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 wrot

[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

[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