[Freesurfer] retinotopy_receptive fields_ STIM PARAMETER

External Email - Use Caution Dear experts, I am performing some study on visual receptive fields (using retinotopy stimuli) and have already run the -recon-all command and it worked fine. After that, I cut the occipital poles (left and right) and flattenend the results. So, now I

[Freesurfer] NIMH-Sponsored Postdoctoral Fellowships in Traumatic Stress Disorders

External Email - Use Caution Collaborating research groups at the VA Boston Healthcare System anticipate up to two NIMH-funded postdoctoral fellowships to begin by September 3, 2020. These training positions are designed to prepare researchers for academically-oriented careers in t

[Freesurfer] TRACULA - input Nifti instead of DICOM?

External Email - Use Caution Hello Anastasia, I am following up on my previous email about running TRACULA on my subject's NIFTI DWI images instead of dicoms and am running into the following issues which I have had before when trying to use NIFTI files instead of dicoms. Too man

Re: [Freesurfer] What's the difference between FSFAST and SPM in the 1-st level GLM?

It is hard to say exactly what the difference is, but in the command below, you set the high-pass cutoff to be 128 Hz meaning that it will try to filter out everything below 128Hz, which is undoubtedly where your signal is. Probably you meant to use something like -hcp .01 or so On 9/27/2019 11

Re: [Freesurfer] mri_surf2vol -lost cluster

You can ask it to sample the maximum along the surface normal over a certain distance. Use --projdist-max. Run mri_vol2surf --help for more info On 9/27/2019 2:04 PM, Albrecht, Daniel S. wrote: Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the fsavera

[Freesurfer] Comparing effects between voxels in a FFX GLM

External Email - Use Caution Hi Doug, I would like to test whether an effect that I observed in a given voxel is larger than in other voxels (this is fMRI data). The additional complication is that I would like to stick as close as possible to the original analysis that yielded the

Re: [Freesurfer] Corpus Callosum area

cd $SUBJECTS_DIR/$subject Sample the aseg onto the surface (looking for the max between -2 and + 2 mm). This will sample all the segmentations, but we are only interested in CC mri_vol2surf --regheader $subject--mov aseg.mgz --projdist-max -2 .5 2 --o lh.aseg.mgz --hemi lh Create a binary map of

Re: [Freesurfer] mask of premotor cortex and primary cortex

Try using 1024 (precentral) and 1022 (postcentral) with the aparc On 10/3/2019 3:11 AM, sang ho shin wrote: External Email - Use Caution Dear Freesurfer Developers, I have analyzed connectivity between striatum and different brain cortex with diffusion weighted MRI. I completed recon-a

[Freesurfer] question on mris_calc - re-submitting

From: Barletta, Valeria Sent: Friday, September 27, 2019 12:30 PM To: freesurfer-boun...@nmr.mgh.harvard.edu Subject: question on mris_calc Dear Freesurfers, I am trying to perform an operation with .mgh files by using mris_calc. This is my operation: (image1

Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area

How did you map the area to fsaverage? If you don't do it properly, you can get some funny results because area has to be jacobian corrected. On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote: External Email - Use Caution Hello all Freesurfer experts! Through my analysis

Re: [Freesurfer] TRACULA - input Nifti instead of DICOM?

There's a line break after: set dcmlist = (APOE.124.dwi.nii.gz APOE.158.dwi.nii.gz APOE.215.dwi.nii.gz APOE.269.dwi.nii.gz From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Daniel Callow Sent: Monday, October 7, 2019 10:21 AM To: Freesurfer support list

Re: [Freesurfer] Question about settig up FS-FAST file hierarchy

The easiest way is to use dcmunpack. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough On 10/5/2019 1:55 PM, Hossein Sanjari Moghaddam wrote: External Email - Use Caution Dear officer, Greetings. We are working on a set of resting-state fMRI data using

Re: [Freesurfer] Confidence interval for Cohen's d from gamma/rstd

You want the 95% CI for Cohen's d itself? I don't know how to do that. If you just want it for the contrast (gamma), then I would just use the formula for a gaussian with mean gamma and stddev sqrt(gammavar) On 10/5/2019 10:43 AM, Caspar M. Schwiedrzik wrote: External Email - Use Cauti

Re: [Freesurfer] Error in glmfit-sim cache

It looks like it might be a locale problem as it thinks that you are inputing "4,0" with a decimal comma instead of a decimal point. Try using "4.0" instead of "4" On 10/5/2019 5:21 PM, Renew Andrade wrote: > External Email - Use Caution > > Dear FreeSurfer experts: > I have an issue wh

Re: [Freesurfer] Comparing effects between voxels in a FFX GLM

I'm not sure what you are trying to do. You want to compare the signal in one voxel vs another voxel in the same map? On 10/7/2019 10:32 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi Doug, I would like to test whether an effect that I observed in a given voxel is lar

Re: [Freesurfer] question on mris_calc - re-submitting

Yes, you can also just use fscalc image1.mgh sub image2.mgh div image2.mgh -o final.mgh On 10/7/2019 10:40 AM, Barletta, Valeria wrote: From: Barletta, Valeria Sent: Friday, September 27, 2019 12:30 PM To: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Vertex by Vertex Analysis

Run mris_preproc with the usual arguments but specify --meas w-g.pct.mgh Then run the rest of the group analysis as if it were a surface file. On 10/4/2019 6:44 PM, WON JONG CHWA wrote: External Email - Use Caution Hello, I would like to perform a group difference analysis with gray-whi

Re: [Freesurfer] question about aparcstats2table

You can create a file called SUBJECTSFILE with all your subjects in it, then run aparcstats2table with the following option --subjectsfile=SUBJECTSFILE On 10/3/2019 11:07 AM, chen wrote: External Email - Use Caution Hi FreeSurfer experts, I want to converts a cortical stats file into a

Re: [Freesurfer] Comparing effects between voxels in a FFX GLM {Disarmed}

External Email - Use Caution exactly Am Mo., 7. Okt. 2019 um 17:15 Uhr schrieb Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>: > I'm not sure what you are trying to do. You want to compare the signal in > one voxel vs another voxel in the same map? > > On 10/7/2019 10:32 AM, C

Re: [Freesurfer] Brodmann area parcellation

You can to run the full recon-all on a given subject's data, and it will create the broadmann areas On 10/5/2019 1:31 AM, sang ho shin wrote: External Email - Use Caution Dear Freesurfer Developers, I am trying to get the seed mask of premotor and motor cortex. Because I can't get it

Re: [Freesurfer] Question about using tkregisterfv to check registration

You can manually change the registration in tkregisterfv. But we rarely see this happen and I'm wondering if it might be some other problem. Are you totally sure that the anatomical and PET come from the same subject? On 10/3/2019 12:59 PM, Vicky Yang wrote: External Email - Use Caution

Re: [Freesurfer] Label created in the symmetric space

Let's backup a moment. Can you send the y.ocn.dat file that has problematic values? On 10/4/2019 4:58 AM, Jose Graterol wrote: External Email - Use Caution Dear Freesurfer Experts, I would appreciate your help. I will explain first what I have done and where my problem is. I want to

Re: [Freesurfer] Comparing effects between voxels in a FFX GLM {Disarmed}

All our tools work independently on different voxels. If you wanted to compare two voxels, you could do it by hand I guess once you had the mean and variance of each measurement at each voxel On 10/7/2019 11:19 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution exactly Am M

Re: [Freesurfer] Brodmann area parcellation

meaning you have to give recon-all the -all switch so it can create things like the lh.white surface cheers Bruce On Mon, 7 Oct 2019, Greve, Douglas N.,Ph.D. wrote: You can to run the full recon-all on a given subject's data, and it will create the broadmann areas On 10/5/2019 1:31 AM, sang

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Thank you for the replay. I think so, I can't find the code 229 in any subject. I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal segmentation and labels. Could it be a problem with the extracerebra

Re: [Freesurfer] Brodmann area parcellation

External Email - Use Caution Dear Douglas, Thank you for your reply.😊 I already ran the full recon-all and I got the results(label, mri, scripts, stats, surf, tmp, touch, trash). But though I tried to get the mask of both brodmann area 4 and 6, I couldn't get the masks. (404BA4a,

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution Hi Douglas, thanks for you answer. I have attached the file to the email. On Mon, Oct 7, 2019 at 5:24 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Let's backup a moment. Can you send the y.ocn.dat file that has > problematic values?

Re: [Freesurfer] Confidence interval for Cohen's d from gamma/rstd {Disarmed}

External Email - Use Caution Ok, thanks! I think the gamma CI will do. Caspar On Mon, Oct 7, 2019 at 17:11 Greve, Douglas N.,Ph.D. wrote: > You want the 95% CI for Cohen's d itself? I don't know how to do that. If > you just want it for the contrast (gamma), then I would just us

Re: [Freesurfer] ERROR gtmseg

Sorry, can you include the previous correspondence so that I know the context? On 10/7/2019 11:45 AM, Marina Fernández wrote: External Email - Use Caution Dear Douglas, Thank you for the replay. I think so, I can't find the code 229 in any subject. I can't see anything strange in the

Re: [Freesurfer] Brodmann area parcellation

when you look in the label file, do you see lh.BA1_exvivo.label lh.BA2_exvivo.label lh.BA3a_exvivo.label lh.BA3b_exvivo.label lh.BA44_exvivo.label lh.BA45_exvivo.label lh.BA4a_exvivo.label lh.BA4p_exvivo.label lh.BA6_exvivo.label On 10/7/2019 11:50 AM, sang ho shin wrote: External Email

Re: [Freesurfer] Label created in the symmetric space

ok, I still don't know what is going on. Can you upload the glmdir and the input to mri_glmfit (ie, the argument of the --y flag). You can upload it using these instructions: From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject N

Re: [Freesurfer] Question about using tkregisterfv to check registration

External Email - Use Caution Hi Doug, I am sure that the anatomical and PET come from the same subject. And I am using the same processing procedures as worked well on other 7 subjects. So I don't think it is because of processing or mixing data. According to the co-registered re

[Freesurfer] Questions re slice thickness, aseg and longitudinal analysis

External Email - Use Caution Freesurfers, First of all, I'd like to express my gratitude to the community for the support that keeps researchers like myself afloat! I have a unique set of oncology patients that I want to evaluate for brain atrophy in a retrospective longitud

Re: [Freesurfer] ERROR gtmseg

External Email - Use Caution Dear Douglas, Sorry! This is the previous information: > Dear Douglas, > > Thank you for the replay. > > I think so, I can't find the code 229 in any subject. > > I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal

Re: [Freesurfer] ERROR gtmseg

We'll have to figure out where those 229s are coming from. Try this mri_binarize --i aseg.presurf.mgz --match 229 --o bin229.mgz It should print out whether there were any voxels that matched. If so, you can load bin229.mgz with the norm.mgz and the aseg.presurf.mgz and see where they are. If the

Re: [Freesurfer] Question about using tkregisterfv to check registration

When you say that you changed the scale, what do you mean? Are you sure that the PET voxel size is accurate? Something else you can try is to specify --dof 9 when you run mri_coreg -- this will fit the scale as well as the translation and rotation. On 10/7/2019 1:51 PM, Vicky Yang wrote:

Re: [Freesurfer] FreeSurfer freezing during processing.

We don't have a lot of experience running recon-all on windows-ubuntu, but I do know that people do so successfully. It does seem weird that mri_em_register is taking over an hour. Do you have a lot of other things running at the same time? If so, try running with just recon-all On 10/3/2019 9:

Re: [Freesurfer] Label created in the symmetric space

External Email - Use Caution Ok, I uploaded it with the name "glmdir.jg.allsubjects.tar.gz". I had to log in as anonymous and not with my email, otherwise it would throw an error (503 Login with USER first. Login failed.). The mgh file is inside the gz file too. Thanks again for yo

Re: [Freesurfer] ECC or non-ECC Memory?

External Email - Use Caution On Mon, 7 Oct 2019 at 02:41, fsbuild wrote: > For this to work, I think the (hardware) memory controller and the CPU need > to support ECC as well. So if the motherboard you are spec'ing out does not > explicitly say it supports ECC, then I would a