[Freesurfer] Trouble with mris_divide_parcellation

External Email - Use Caution I am having some trouble with mris_divide_parcellation. When I follow the procedure in —help, my input and output annotations appear to be identical. The input annotation consists of 5 labels that I’m trying to divide into either 2 or 3 regions. The

[Freesurfer] Unable to unsubscribe {Disarmed}

External Email - Use Caution Hello, When I go to http://secure-web.cisco.com/1jgCpVnCnpYUf1STtrprTp2p1sr_-sFIyb-fzDa-XLhkXgR0pWQKQfhkzlnCizG-S8rzdd1hy5polLzaMxstD3v2iLx6Lt6eyimfo3QaSCfCqxwEWExH8w1zlsgl03R5YQBxXnHy3cGlrO1ip_FiPeosoH-KRj1LfWHqprl6937Qj4MGNvbVpmt4RmlaoKb_L11GGKbiP2M

[Freesurfer] linkedUbuntu 18 virtual disk image - Developer password {Disarmed}

External Email - Use CautionDear All, I have exactly the same question as Miguel, could you sent me the password as well?  Thank you and kind regards, Amice -- Forwarded message -Van: fsbuild Date: di 15 dec. 2020 om 00:11Subject: Re: [Freesurfer

Re: [Freesurfer] group analyses

yes, run mris_preoproc with --meas volume, then surf2surf. Then run mri_segstats --i lh.volume.mgz --exludeid 0 --seg ocn.mgz --avgwf avgwf.dat --accumulate where lh.volume.mgz is the output of rerunning mris_preproc above ocn.mgz is the ocn file which is output from the cluster analysis avgwf.d

Re: [Freesurfer] asegstats2table

If you use mris_anatomicalstats to create the stats file (in the stats folder), then use aparcstats2table to create a table from multiple subjects On 12/11/2020 6:57 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Hello Freesurfers, I have a question about the command ase

Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

There have been some changes that are breaking your stream. Try this cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i

Re: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!

Hard to say without the recon-all.log file, but my guess is that something is wrong with one of your surfaces. Load the surfaces in freeview and see how they look On 12/14/2020 7:30 PM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Hi there, Hope this finds you well I ha

Re: [Freesurfer] How to remove clusters less than 50 vertex/voxels in FreeSurfer during visualisation

You can add --minarea XXX to your mri_surfcluster command line where XXX is the minimum area in mm2 On 12/15/2020 8:33 AM, Sunil Khokhar wrote: External Email - Use Caution Dear Experts! After doing the statistics I want to remove clusters that are less than 50 voxels/vertices from si

Re: [Freesurfer] Error During Fix Topology and Brain Usability

I don't think it is worth doing a surface-based analysis on this subject. The subcortical may be salvageable On 12/16/2020 11:55 AM, Angel Hammond wrote: External Email - Use Caution Dear Experts, I have a brain that I have been getting an error for during fix topology during recon-al

Re: [Freesurfer] fspalm error : --sig2p-max unknown

You need the patch. See the docs here https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm under Setting Up On 12/16/2020 2:02 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, When I was running permutations with fspalm an error appeared because it couldn't find the

Re: [Freesurfer] FREESURFER AND NEURONAVIGATOR IMAGE

Sorry, we don't have anything that will do this. I know there are a few out there that will do it, but I don't know their names off hand. Maybe 3D slicer. On 12/17/2020 4:20 AM, marco.m...@tin.it wrote: External Email - Use Caution I need to use freesurfer bra

Re: [Freesurfer] Multiple Frames

What are the 2 frames? You could extract the first or the second or average them or compute an RMS, but it depends on what is there On 12/17/2020 2:03 PM, Hsieh, Stephanie wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

Re: [Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

Is the lh.orig surface changing? On 12/17/2020 5:53 PM, Ben Deen wrote: External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to recon

Re: [Freesurfer] Extracted mean timecourse from FS label {Disarmed}

Sorry, I don't know the best way to test it. You might ask the fmriprep people On 12/18/2020 7:05 AM, Mason Wells wrote: External Email - Use Caution Hi Doug, The waveforms look OK to me but was worried that the message was suggesting the command was not suitable with GIFTI data. Is th

Re: [Freesurfer] error message when running mri_info

You can see that the vox_units are Unknown in the fslhd output. This is the source of the problem in FS. On 12/18/2020 10:53 AM, Jonathan Lynn wrote: External Email - Use Caution Hello, I've been using a software to process SWI data that includes an option to save the output as nifti

Re: [Freesurfer] Failed tissue type check {Disarmed}

Try adding --replace 29 2 to your command line On 12/18/2020 12:07 AM, Julie Ottoy wrote: External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to no

Re: [Freesurfer] Failed tissue type check {Disarmed}

You can use the fix from my previous email or you can add the following line any were into the gtmseg.ctab file: 29 Left-undetermined 135 206 235 0 3 On 12/18/2020 11:06 PM, Julie Ottoy wrote: External Email - Use Caution Sorry I would like to correct my previou

Re: [Freesurfer] error in running tkregisterfv

tkregisterfv requires an LTA file. Try running bbregister with an LTA output, eg, bbregister --s subject_30_8_2020 --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.lta --init-header –bold On 12/20/2020 5:03 AM, Peter de Best wrote:

Re: [Freesurfer] Converting a binary volume roi.nii file to a label for roi analysis in Freesurfer

Run recon-all on the MNI template, then view your ROI on the output volume, including the surfaces to verify that the surfaces pass through your ROI. Map the ROI to the surface using mri_vol2surf with the --regheader option, then map the surface-ROI to each subject with mris_apply_reg (make sure

Re: [Freesurfer] Can't find Mindboggle datasets

don't know, try asking the people at mindboggle On 12/21/2020 3:40 AM, 1248742467 wrote: External Email - Use Caution Hello, everyone In mindboggle website, the data is freesurfer-output, But I just want to download the 101 source data, use recon -all command preprocess them by myself.

Re: [Freesurfer] how to use recon-all command

Try looking at our tutorials on how to get started http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials but you can start by running recon-all -s your-first-subject -i T1.nii.gz -all On 12/21/2020 4:03 AM, 1248742467 wrote: External Email - Use Caution Hello, everyone my freesurfer enviro

Re: [Freesurfer] Error in selxavg3-sess {Disarmed}

Can you send the full terminal output? Do all subjects have the same paradigm files? On 12/21/2020 5:24 AM, Nina Khatibi wrote: External Email - Use Caution No, I have checked them all. On Thu, Dec 17, 2020 at 6:05 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Are

Re: [Freesurfer] fspalm contrasts {Disarmed}

Oh, sorry, I did not include that as a possibility. FSL codes F-contrasts differently than t-contrasts (FS codes them in the same way, just a matrix). If you want to do it this way, you'll have to use PALM by itself without the fspalm frontend. fspalm should still create files that can be conven

Re: [Freesurfer] Anterior insula thickness

We don't have an anterior insula segmentation. One thin you can try is to divide the insula label with mris_divide_parcellation. If one of those subdivisions works for you then you can compute the thickness inside it. You might want to do it on fsaverage and then map it back to the individual s

Re: [Freesurfer] monkey atlas D99 {Disarmed}

The argument to the --label flag should be a freesurfer label file, this is a text file not an nii.gz file. On 12/21/2020 10:52 AM, Francesca Strappini wrote: External Email - Use Caution Thank you! I run mri_label2vol but I got this error. mri_label2vol --label D99_atlas_in_NMT_v2.0_a

Re: [Freesurfer] PFC segmentation

Do you want a binary map? If so, you can run mri_binarize --i aparc+aseg.mgz --o pfc.mgz --match Id1 Id2 ... where Id1 ... is a list of segments you want in your binary map as found in $FREESURFER/FreeSurferColorLUT.txt, eg, 1028 is left superior frontal 1028ctx-lh-superiorfrontal

Re: [Freesurfer] Non-uniform voxel size

No, not a problem. On 12/21/2020 12:52 PM, Julie Ottoy wrote: External Email - Use Caution Dear freesurfer team, I am dealing with PET scans that were acquired at different sites. They do not have uniform voxel size and dimensions. I was wondering if this would be an issue for the sG

Re: [Freesurfer] Vertex-wise functional ROI extraction

We don't have anything that creates a text file of the time course in each voxel, if that is what you mean. In principle you can do it in matlab... On 12/21/2020 4:28 PM, Sussman, Lauren wrote: > External Email - Use Caution > > Hello! > > I would like to extract functional data from a

Re: [Freesurfer] Talairach Failure in recon-subject {Disarmed}

That is just the failure detection. Sometimes it generates a false positive. Did you check the transform? If the rest of the downstream processes (eg, aseg and surfaces) are ok, then you don't need to worrry On 12/21/2020 6:53 PM, Wei Shao wrote: External Email - Use Caution Hi, Freesu

Re: [Freesurfer] cluster size and FWER rough equivalence?

On 12/21/2020 8:45 PM, Kayle Sawyer wrote: External Email - Use Caution We are working on a manuscript revision for an fMRI project that was analyzed with FS-FAST 5.3 years ago. We used mri_glmfit, and then we ran mri_surfcluster (instead of mri_glmfit-sim) with a vertex-wise threshol

Re: [Freesurfer] No extracerebral CSF in sGTM

yes, it does, assuming the segmenation of extra cerebreal CSF is adequate On 12/22/2020 12:57 AM, Julie Ottoy wrote: External Email - Use Caution Dear Petsurfer team Does the sGTM PVC correct for the uptake in extra cerebral CSF? If not, how would this affect the reliability of the cort

Re: [Freesurfer] Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory

Try using RB_all_2016-05-10.vc700.gca instead On 12/22/2020 5:54 AM, Camerino, I.L. (Ileana) wrote: ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon labels.DKT31.manual.nii.gz appears ERROR: Talairach failed

Can you send the recon-all.log file? On 12/22/2020 7:23 AM, 1248742467 wrote: External Email - Use Caution Hello, everyone I have download the labels.DKT31.manual.nii.gz in mindboggle datsets, I want to use recon-all command to get lh.labels.DKT31.manual.annot. But, when I run: recon-a

Re: [Freesurfer] Error

Source 7.1.1 Go into $SUBJECTS_DIR rm fsaverage ln -s $FREESURFER/subjects/fsaverage that should do it On 12/22/2020 8:47 AM, Weerasekera, Akila wrote: Hello, I sent a few jobs to launchpad (FreeSurfer segmentation) and they exited with an exit=1, this is the error: "ERROR: Label FG1.mpm.vpnl d

Re: [Freesurfer] Question about a feature introduced in FS 7.0

I don't have any example, but the idea is pretty simple. If you want to freeze a point on the surface, open aseg.presurf.mgz and the surfaces for your subject, eg, tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs Then edit the aseg.presurf.mgz to change the voxels where you want to freeze to

Re: [Freesurfer] linkedUbuntu 18 virtual disk image {Disarmed}

External Email - Use Caution Hello Amice, The info has been sent to your email address. -R. On Dec 23, 2020, at 07:20, C. Teurlings wrote:External Email - Use CautionDear All, I have exactly the same question as Miguel, could you sent me

[Freesurfer] Please remove me from the email list

External Email - Use Caution ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] monkey atlas D99 {Disarmed}

External Email - Use Caution Ok thanks. I need to extract the mean signal from the regions contained in this nifti file. I suppose I need first to resample it in functional space and then use mri_segstats, but I'm not sure which is the right way to do it. Any suggestion? On Wed,