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17 participants
30130 discussions

"error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"
by Ludmila Midrigan 17 Nov '23

17 Nov '23

External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast" I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3 I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much! *milly mc * *"Life is a foreign language; all mispronounce it." * *Christopher Morley*

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Unable to run recon-all
by Nai, Ying Hwey 17 Nov '23

17 Nov '23

External Email - Use Caution Dear Freesurfer personnel, I downloaded and installed the latest version successfully following the instructions on windows WSL. However, I could not run recon-all. I then installed an older version, but I still could not run the recon-all. Could you please kindly advise me on how to resolve this issue? Thank you. Regards, Ying Hwey ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Segmentation of hippocampal subfields and nuclei of the amygdala
by Joshua Ezequiel Pasaye 17 Nov '23

17 Nov '23

External Email - Use Caution Hello, I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso, ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence. Please let me know if you need additional information. Thanks, Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pasaye(a)northwestern.edu<mailto:joshua.pasaye@northwestern.edu>

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Running autorecon2-wm after wm edits makes no difference in final surface
by Fernanda Hansen P. de Moraes 17 Nov '23

17 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3 nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Here attached is the complete recon-all log file from the beginning, including all steps attempted. I would be very glad if you could help me overcoming this error to include as much subjects as possible in my project. Best regards, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com<mailto:fernandahmoraes@gmail.com> Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Hippocampal subfields segmentation
by yunus soleymani 17 Nov '23

17 Nov '23

External Email - Use Caution Hello Freesurfer users, I was wondering if there is any Freesurfer code available for performing hippocampal subfield segmentation on multiple subjects simultaneously in parallel. I already have the code for analyzing a single subject, but I'm interested in analyzing hundreds of subjects at once. Thank you very much. Best regards,Yunus

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Mapping input volume (fa.nii) to hippocampus segmentation volume
by Mirsol Choi 16 Nov '23

16 Nov '23

External Email - Use Caution Hello Freesurfers, I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area. I am able to segment the hippocampus using the command (segmentHA_T1.sh) and I was also able to perform the dt-recon function on dwi data. I am trying to map the fa.nii file from dt-recon into the hippocampus subfield volume rh.hippoAmygLabels-T1.v22.HBT.mgz, however when I run the code that is provided by vol2subfield -help: vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta or vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz I am met with a message stating "set: Variable name must contain alphanumeric characters." How can I fix this "variable name must contain alphanumeric characters" issue and run this command? Thank you all for your time, help and expertise. M

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Downloading OVA
by Tellis, Wyatt 16 Nov '23

16 Nov '23

External Email - Use Caution Hi, I'd like to download the OVA to run in VirtualBox, but the wiki article (https://secure-web.cisco.com/14mYPNciAyjJLQ-z9NWag-roFmGKjbtQeqtDD8X-3yq9rT…) says its being updated: As of 09/11/2023 he (sic) VM image is currently being updated and the link to it will be restored when the update is complete. Is there an estimate for when the new OVA will be released? Thanks, Wyatt

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Question about lesions output
by reza razmara 16 Nov '23

16 Nov '23

External Email - Use Caution Hi freesurfer I did an experiment about lesions about the output of samseg. And the results are as follows: The volume of lesions in label 99 in seg.mgz result is 745 mm^3. The samseg output for lesions in samseg.stats is 633 mm^3. Is it ok? Why are they different? Thanks for your help

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Problem with brainstem overlap after BBR
by Spapens, Jeltje (NP) 16 Nov '23

16 Nov '23

External Email - Use Caution Hello Freesurfer Developers, I have performed a boundary-based registration followed by a mri_vol2vol on a Neuromelanin sensitive MRI scan (partial FoV) with a T1 structural scan. I used this code: Boundary-based registration in Freesurfer Set the environment in the terminal. bbregister --s MRS_203_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz --reg MRS_203_NM2mp2rage.dat --T1 --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_stripped.mgz --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_upsamp.nii --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_203/MRS_203_MT_tfl_regt1.nii.gz --reg MRS_203_NM2mp2rage.dat –cubic I performed the analysis on two participants, but the brainstem does not overlap very nicely. I attached the screenshots of Freeview of the two participants with the T1 scan and the NM scan after the BBR. Our analysis focuses on the Substantia Nigra. I also attached the full script that we use including the pre analysis. Do you have a tip how to improve the BBR to reach better overlap. Kind regards, Jeltje Spapens

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Issue with PALS_B12_Brodmann.annot Labels in FreeSurfer
by Xinjie Chen 16 Nov '23

16 Nov '23

External Email - Use Caution Dear FreeSurfer Team, I am writing to report a significant issue I have encountered while using the PALS_B12_Brodmann.annot files in FreeSurfer. I have noticed a critical error concerning labeling certain Brodmann areas. Specifically, in the left hemisphere, labels such as Brodmann area 33, CON_deeper_than_WS_t_2', and ASP deeper' appear to share the same label ID. Similarly, in the right hemisphere, the label for Brodmann area 3 seems to be merged with Brodmann area 33. This overlap of labels and the lack of unique IDs for distinct Brodmann areas like Brodmann 3 and Brodmann 33 are causing significant confusion and potential errors in analysis. For instance, this issue complicates tasks such as calculating variables for individual Brodmann areas, leading to inaccurate results. I am keenly interested in any solutions or methods you could suggest for resolving this problem. Thank you in advance for your assistance and I am looking forward to a resolution. Best regards, Xinjie

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