[Freesurfer] Error with write_annotation program !

External Email - Use Caution Hi FreeSurfer experts, I am trying to run write_annonation program in MATLAB and getting following error: >> [v, L, ct] = read_annotation('lh.Yeo2011_7Networks_N1000.annot'); >> ct.table(1:6,1:3) = 1; >> write_annotation('lh_Yeo2011_DMN',v,L,ct); Erro

Re: [Freesurfer] Help with LGI

If you type matlab at the command line, does matlab start? On 7/12/2020 10:42 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, I have added Matlab my path and either the same er

Re: [Freesurfer] Segmentation with FreeSurfer 7.1

I don't. My guess is that there is a tolpolgical default there that is not fixed correctly in 7.1. Sometimes these things are on the edge and slight changes will affect them. On 7/13/2020 4:22 AM, Sara PONTICORVO wrote: External Email - Use Caution Dear FreeSurfer experts, we are pe

Re: [Freesurfer] aparcstats2table error

External Email - Use Caution Hi Devika, I ran into the same issue and in case you don’t want to change your PATH (like me), another option is to edit aparcstats2table script and simply replace the shebang from “#!/usr/bin/env python” to e.g. “#!/usr/bin/env python2” (please make

Re: [Freesurfer] mri_aparc2aseg with flag --a2005s

We don't have labels for those. The LUT is aspirational at times. Just because something is in the LUT does not mean that we label it. On 7/13/2020 8:01 AM, Anja Samardzija wrote: External Email - Use Caution Hi, I was wondering if you have any updates on this (getting the ctx-lh-pr

Re: [Freesurfer] ROI-wide cortical thickness for each network !

If you have the Yeo atlas in the individual space, you can use mris_anatomical_stats to compute stats the same as in the Desikan atlas. Look in recon-all.log for the command line and customize it as needed On 7/14/2020 5:00 PM, Martin Juneja wrote: External Email - Use Caution Hi e

Re: [Freesurfer] Error with write_annotation program !

Does it work if you take out that change to ct.table? On 7/15/2020 3:34 AM, Martin Juneja wrote: External Email - Use Caution Hi FreeSurfer experts, I am trying to run write_annonation program in MATLAB and getting following error: >> [v, L, ct] = read_annotation('lh.Yeo2011_7Netwo

Re: [Freesurfer] Error with write_annotation program !

External Email - Use Caution I tried reading and writing lh.aparc.annot of bert, and it works ONLY if you change the output filename by adding a file extension. Try write_annotation('lh_Yeo2011_DMN.annot',v,L,ct); Tim > On July 15, 2020 at 3:56 PM "Douglas N. Greve" wrote

[Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects

External Email - Use Caution Dear list, As described by others on this list, recon-all with Freesurfer 7.1 on a Mac operating system seems to fail for around 10% of the subjects. The following solution was offered: sudo curl https://raw.githubusercontent.com/freesurfer/freesur

Re: [Freesurfer] Label on fsaverage failure

On 7/15/2020 10:59 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Douglas and Bruce, on the same subject, I wanted to ask two questions: 1. since the ROIs were obtained on 2mm voxels, is the command $ mri_vol2surf --mov ROI_set1/LeftAngG.img--regheader MNI_1mm --interp

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution Hi All, Just in case the below poster was missed. Thanks, Xiaomin From: Xiaomin Yue Sent: Saturday, July 11, 2020 1:43 PM To: Freesurfer support list Subject: [Freesurfer] mri_fieldsign

Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects

Can you send the recon-all.log file for some of the failures? On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote: External Email - Use Caution Dear list, As described by others on this list, recon-all with Freesurfer 7.1 on a Mac operating system seems to fail for around 10% of the

Re: [Freesurfer] mri_fieldsign error

I don't know what is going wrong here. One simple thing to check is to make sure that all the input files have the same number of vertices as the surface. If that is the case, then upload the subject and input files using the instructions below From the linux command line, Create the file you

[Freesurfer] Extracting PET Binding Values from Inflated Surface

External Email - Use Caution Hi Doug, I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have been first transformed into FS subject space, mapped to the cortical surface using mri_vol2surf (signal averaged over the middle 80% of the corti

[Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

External Email - Use Caution Dear freesurfer experts I was able to run the same subects on the longitudinal stream using FS 6 , but when I use FS7.1 I got this error RROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! ERROR: @#@FSTIME 20

Re: [Freesurfer] ROI-wide cortical thickness for each network !

External Email - Use Caution Dear Doug, Thanks for your response ! Yes, I have Yeo atlas in the individual space, and recon-all.log has the following command: mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.anno

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution Hi Doug, The file LOO.tar.gz has been uploaded to transfer/incoming directory on the ftp server. Please let me know what else you need to solve this problem. Thanks, Xiaomin From: Douglas N. Greve Sent: Wednesday, Ju

Re: [Freesurfer] Label on fsaverage failure

External Email - Use Caution Dear Douglas and Bruce,on the same subject, I wanted to ask two questions:1. since the ROIs were obtained on 2mm voxels, is the command  $ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out Left_AngG

Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

External Email - Use Caution Hi Eugenio, I am having trouble uploading the file through FTP. Can you send me an email to send the file to using the Martinos Center File Drop? Thanks, Jenna ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] TRACULA preprocessing error

Hi Jason - Did this file get created? /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Jason Silva Rudberg Sent: Sunday, July 12, 2020 2:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject:

[Freesurfer] Cortical Parcellations in FreeSurfer 7

External Email - Use Caution Dear Freesurfer Developers, I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer: - Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROI

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

External Email - Use Caution It ran on a computer with CentOS Linux release 7.8.2003 (Core) and Freesurfer was build using easybuild by the cluster support staff. Knut Jørgen On 15/07/2020 19:51, Knut J Bjuland wrote: External Email - Use Caution Dear freesurfer expe