Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Hypothalamic subunits segmentation yields different results in versions 7.2.0 and 7.4.1
by Maria Paternina Die 15 Apr '25

15 Apr '25

External Email - Use Caution Dear all, I am running the mri_segment_hypothalamic_subunits module on a longitudinal dataset. As a quality control step, I have been removing those subjects for whom the output volume of any subunit is exactly zero, assuming that the segmentation failed for those cases. I have run this with FreeSurfer versions 7.2.0 (with the --threads flag enabled to 4) and 7.4.1 (without the --threads flag, as it caused the process to fail). From my 1,732 subjects, using the exclusion criteria of zero-volume in any subunit: - With version 7.2.0, I had to exclude about 17% of subjects. - With version 7.4.1, this number jumps to 72%. My question is: why is the latest version (7.4.1) producing so many 0 in some subunits? I’ve seen that some changes were introduced to this module in version 7.3.2. I believe this issue might be related to the following thread on the mailing list: https://secure-web.cisco.com/1XkIk65tX0PeiP2O9MZLgv1T5LO0ub4C7O1QmkU5Ce9f35… As additional information, we are running over ubuntu (24.04.2). The version 7.2.0 was installed with the deb installer and the version 7.4.1was the compiled one (tar.gz). The subunits with more 0 values are the anterior-inferior, posterior, and anterior-superior but also we found 0 in the tubular subunits, Many thanks for your help! Sincerely, *María Paternina Die* *Grupo de Neuroimagen, * *Hospital General Universitario Gregorio Marañón,* *Madrid, Spain* *Google Scholar: María Paternina-Die* *Website:https://secure-web.cisco.com/1g00gucsTRfBUHoFwCMckaiWl-XXgR4anWnA0N2hNTMX1Oyld05_nOH5knqLQ55m49-uPh62hII0ZFAsLy16YUwvaw7dd_4beDxHSue6_Vn5cGxSKDtKnzQvZhZlgvPGHswFqu9gqrqbfW0S3mBT3AEfZ3xAE6i1Ol_p8luGDA8zOpICAYDd9PEPaZ-N2zowKEPU5eNrLviBTjMTprN3ww90dZaraK1fcsZfBDNP5Wf53NA8Yoy-gbNtqJnClDURAGAo-OW92CYVkv26aTG1CuhMlkls6n-UsK7R_ZbMrkMGaT42vyEXfkLMLx7bhGL0c/https%3A%2F%2Fneuromaternal.es <https://secure-web.cisco.com/18fzi4Ql2j271hl0quVZhU9HPdWC0xf-x7Zs8qwrDJzvsR…>* -- *Este mensaje y sus archivos adjuntos son confidenciales y únicamente podrán ser usados por la persona o entidad a la que van dirigidos. Este mensaje puede contener información confidencial o legalmente protegida. No hay renuncia a la confidencialidad o secreto profesional por cualquier transmisión defectuosa o errónea. Si usted ha recibido este mensaje por error notifíqueselo inmediatamente al remitente. Le informamos que los datos personales que usted nos ha proporcionado son tratados por FUNDACIÓN PARA LA INVESTIGACIÓN BIOMÉDICA DEL HOSPITAL GREGORIO MARAÑÓN, domiciliada en la calle Doctor Esquerdo 46, Pabellón de Gobierno, planta baja, 28007 de Madrid con la finalidad de gestionar y mantener las relaciones profesionales que nos unen con Usted. Sus datos podrán ser comunicados a las entidades y administraciones públicas necesarias para la realización de dicha gestión. Este tratamiento de datos es necesario para mantener dicha relación profesional. Los datos se eliminarán cuando finalicen los plazos de prescripción marcados por la ley, conservándose únicamente para atender posibles reclamaciones. Ud. puede ejercer sus derechos de acceso, rectificación, cancelación, oposición, portabilidad y limitación del tratamiento de sus datos dirigiéndose a FUNDACIÓN PARA LA INVESTIGACIÓN BIOMÉDICA DEL HOSPITAL GREGORIO MARAÑÓN, a la dirección calle Doctor Esquerdo 46, Pabellón de Gobierno, planta baja, 28007 de Madrid, o vía correo electrónico al email gerencia(a)fibhgm.org <mailto:gerencia@fibhgm.org>, acompañando copia de su DNI acreditando debidamente su identidad. En cualquier situación, Ud. tiene derecho a presentar una reclamación ante la Agencia Española de Protección de Datos (AEPD). Datos Delegado de Protección de Datos (DPO) de FUNDACIÓN PARA LA INVESTIGACIÓN BIOMÉDICA DEL HOSPITAL GREGORIO MARAÑÓN: Alaro Avant, S.L. Avda. de Brasil 17, 7C, 28020, Madrid dpo.fibgregoriomaranon(a)alaroavant.com <mailto:dpo.fibgregoriomaranon@alaroavant.com> 9**14265115*

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Problem with aparcstats2table
by Rosalia Dacosta Aguayo 15 Apr '25

15 Apr '25

External Email - Use Caution Dear Freesurfer team, I am having a trouble with aparcstats2table I have never seen before and I do not know how to solve it. I have run it with --help and still I don't quite understand it. Any help would be appreciated. Kind regards, Rosie rosalia@rosalia-Lenovo-Y520-15IKBN:~/Desktop/CAN_RUTI$ aparcstats2table --hemi rh --subjects sub-012_ses-BSL sub-012_ses-FU1 sub-012_ses-FU2 sub-013_ses-BSL sub-013_ses-FU1 sub-013_ses-FU2 sub-014_ses-BSL sub-014_ses-FU1 sub-014_ses-FU2 sub-015_ses-BSL sub-015_ses-FU1 sub-015_ses-FU2 sub-016_ses-BSL sub-017_ses-BSL sub-017_ses-FU1 sub-017_ses-FU2 sub-019_ses-BSL sub-019_ses-FU1 sub-019_ses-FU2 sub-020_ses-BSL sub-020_ses-FU1 sub-020_ses-FU2 sub-021_ses-BSL sub-021_ses-FU1 sub-021_ses-FU2 sub-022_ses-BSL sub-022_ses-FU1 sub-022_ses-FU2 sub-023_ses-BSL sub-023_ses-FU1 sub-023_ses-FU2 sub-024_ses-BSL sub-024_ses-FU1 sub-024_ses-FU2 sub-025_ses-BSL sub-028_ses-BSL sub-028_ses-FU1 sub-029_ses-BSL sub-029_ses-FU1 sub-029_ses-FU2 sub-030_ses-BSL sub-030_ses-FU1 sub-030_ses-FU2 sub-031_ses-BSL sub-031_ses-FU1 sub-031_ses-FU2 sub-032_ses-BSL sub-032_ses-FU2 sub-033_ses-BSL sub-033_ses-FU1 sub-033_ses-FU2 sub-034_ses-BSL sub-034_ses-FU1 sub-035_ses-BSL sub-035_ses-FU1 sub-035_ses-FU2 sub-036_ses-BSL sub-036_ses-FU1 sub-036_ses-FU2 sub-037_ses-BSL sub-038_ses-BSL sub-038_ses-FU1 sub-038_ses-FU2 sub-039_ses-BSL sub-039_ses-FU1 sub-039_ses-FU2 sub-040_ses-BSL sub-040_ses-FU1 sub-040_ses-FU2 sub-041_ses-BSL sub-041_ses-FU1 sub-041_ses-FU2 sub-042_ses-BSL sub-042_ses-FU1 sub-043_ses-BSL sub-044_ses-BSL sub-045_ses-BSL sub-046_ses-BSL sub-046_ses-FU1 sub-046_ses-FU2 sub-047_ses-BSL sub-047_ses-FU1 sub-047_ses-FU2 sub-048_ses-BSL sub-051_ses-BSL sub-051_ses-FU1 sub-051_ses-FU2 sub-053_ses-BSL sub-054_ses-BSL sub-054_ses-FU1 sub-054_ses-FU2 sub-055_ses-BSL sub-055_ses-FU1 sub-056_ses-BSL sub-056_ses-FU1 sub-056_ses-FU2 sub-057_ses-BSL sub-058_ses-BSL sub-058_ses-FU1 sub-058_ses-FU2 sub-059_ses-BSL sub-060_ses-BSL sub-060_ses-FU1 sub-060_ses-FU2 sub-061_ses-BSL sub-061_ses-FU1 sub-061_ses-FU2 sub-062_ses-BSL sub-062_ses-FU2 sub-063_ses-BSL sub-064_ses-BSL sub-064_ses-FU1 sub-064_ses-FU2 sub-065_ses-BSL sub-065_ses-FU1 sub-065_ses-FU2 sub-067_ses-BSL sub-068_ses-BSL sub-068_ses-FU1 sub-068_ses-FU2 sub-069_ses-BSL sub-070_ses-BSL sub-070_ses-FU1 sub-070_ses-FU2 sub-071_ses-BSL sub-072_ses-BSL sub-072_ses-FU1 sub-072_ses-FU2 sub-073_ses-BSL sub-074_ses-BSL sub-074_ses-FU1 sub-074_ses-FU2 sub-075_ses-BSL sub-075_ses-FU1 sub-075_ses-FU2 sub-076_ses-BSL sub-077_ses-BSL sub-077_ses-FU1 sub-077_ses-FU2 sub-078_ses-BSL sub-079_ses-BSL sub-079_ses-FU1 sub-079_ses-FU2 sub-080_ses-BSL sub-080_ses-FU1 sub-080_ses-FU2 sub-081_ses-BSL sub-082_ses-BSL sub-082_ses-FU1 sub-082_ses-FU2 sub-083_ses-FU1 sub-083_ses-FU2 sub-084_ses-BSL sub-084_ses-FU1 sub-084_ses-FU2 sub-085_ses-BSL sub-085_ses-FU1 sub-085_ses-FU2 sub-086_ses-BSL sub-086_ses-FU1 sub-086_ses-FU2 sub-087_ses-BSL sub-087_ses-FU1 sub-087_ses-FU2 sub-088_ses-BSL sub-088_ses-FU1 sub-088_ses-FU2 sub-089_ses-BSL sub-089_ses-FU1 sub-089_ses-FU2 sub-090_ses-BSL --meas thickness --tablefile aparc-stats-thickness.txt *ERROR: Specify one of --subjects, --subjectsfile --qdec or --qdec-long* or run with --help for help. ____________________________________________________________________________ Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

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missing region when annotating pial surface with Yeo400
by Simone Cauzzo 15 Apr '25

15 Apr '25

External Email - Use Caution Dear support I want to put the Yeo 400 annotations on my recon-all output and produce a volume. I'm using the following commands: mri_surf2surf --srcsubject fsaverage --trgsubject subj[..] --hemi rh --sval-annot [...]/Yeo_fsaverage/label/kong17/rh.400Parcels_Kong2022_17Networks.annot --tval [...]/rh.aparcYeo.annot [same for LH] mri_surf2volseg --o [...]_aparc+aseg_yeo.mgz --label-cortex --i mri/aseg.mgz --srcmri/aseg.mgz --threads 4 --lh-annot label/lh.aparcYeo.annot 0 --lh-cortex-mask label/lh.cortex+hipamyg.label --lh-white surf/lh.white --lh-pial surf/lh.pial --rh-annot label/rh.aparcYeo.annot 200 --rh-cortex-mask label/rh.cortex+hipamyg.label --rh-white surf/rh.white --rh-pial surf/rh.pial The annotations come from Yeo_fsaverage/label/kong17/lh.400Parcels_Kong2022_17Networks.annot as downloaded from the link in the paper published. For some reason, left hemisphere region 17networks_LH_DefaultC_PHC_2 is not present in the resulting volume. The region is just set to zero as if it was masked out. I thought about something wrong with the recon all output but this happens for all my subjects, and the recon-all output looks ok. Am I missing something? Simone Cauzzo

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Hausdorff distance
by Davide Sabbadin 15 Apr '25

15 Apr '25

External Email - Use Caution Hi all, I am trying to compute the Hausdorff distance between a binary mask and all the ROIs in the atlas (cvs_avg35_inMNI152), in order to identify the closest ROIs to the mask. To better account for the folding behavior of the cortical surface, I would like to use *geodesic distance* as the metric instead of the Euclidean one. Is there an easy way to compute this? Thanks in advance! Best regards, Davide

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Help with group over time analysis in FreeSurfer (Repeated Measures ANOVA)
by Emilia Rydén 14 Apr '25

14 Apr '25

External Email - Use Caution Hi everyone, I’m new to FreeSurfer and currently working on a group-by-time analysis. I have two groups (language and control) and two time points (pre and post). I’m planning to run a repeated measures ANOVA using the approach described here: https://secure-web.cisco.com/17-MXDv-625h05yLHVA36RwisjCP6uV-tVc6FhAka3PqeN… I’ve attached my initial attempt at an FSDG file. I would greatly appreciate any guidance on how to correctly model this, particularly when it comes to setting up the contrast files. Thank you in advance for your help! Best regards, Emilia

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Feasibility and Accuracy of Using SAMSEG with ADC Maps
by Taghizadeh Mortezaei, Nima 13 Apr '25

13 Apr '25

Dear FreeSurfer team, I am currently using FreeSurfer v7.4.1 and I want to ask is it feasible to run SAMSEG directly on ADC maps derived from diffusion MRI for segmenting normal brain anatomy? Alternatively, would it be more accurate to perform segmentation on a T1-weighted image and then transfer the labels to the co-registered ADC image? Thank you very much for your time and support. Best regards, Nima

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Re: [Freesurfer] Updates/bug fixes available for the 8.0.0 release
by fsbuild 11 Apr '25

11 Apr '25

External Email - Use Caution For ubuntu Linux the release string should be 8.0.0 and not 8..0.0, i.e., On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh On Apr 11, 2025, at 20:24, fsbuild <fsbuild(a)contbay.com> wrote:On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8..0.0  bash  fs8_updates.sh

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trac-preproc: orientLAS and mri_info issue with unsigned shorts
by Mirro, Amy 11 Apr '25

11 Apr '25

External Email - Use Caution Hi, Thanks so much for all your work on Freesurfer. I am currently running tracula v7.4 and I am coming across the following error. I believe this error is occurring during the orientLAS call in trac-preproc (the output is copied from my log file): orientLAS /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 awk: cannot open is (No such file or directory) awk: cannot open is (No such file or directory) awk: cannot open is (No such file or directory) mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz I think the error in orientLAS might be due to the mri_info calls inside orientLAS (starting around here: https://secure-web.cisco.com/1yGfA9jbEQb9uMtyDf5LggAJmO-aUQoPIO34H0YN-0Lu0i…) When I attempt to run mri_info on my niftis, I get the following warning : "INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k -1 -0 0" I think that when mri_info returns this warning inside the orientLAS code, it causes orientLAS to fail, since the xyzR, xyzA, and xyzS variables are not set as expected. Do you have any suggestions on how I could solve this? Is there perhaps a way to suppress the warning in mri_info? Or is there a straightforward way to convert unsigned short data? Thanks, Amy ________________________________ 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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mris_register external atlas
by Stefanie Bradley 10 Apr '25

10 Apr '25

External Email - Use Caution Hi there, I am trying to register my Freesurfer subject's cortical surface into a common space to use the parcellations from a pediatric atlas (UNC 4D cortical surface atlas). With Freesurfer version 8.0.0 in a Linus OS, I am using mris_register as: mris_register -1 individual_subject/lh.sphere 4D_atlas/lh.sphere individual_subject /lh.sphere.FS.reg. I am getting an error where it says it requires a smoothwm file from the atlas files, though I only have curvature and sphere files from the atlas. Is there a way to register the atlas files to my subjects and then put the parcellations onto my subject's cortical surface? Thanks, Stefanie

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Re: [Freesurfer] nu_correct error: Can't locate Sys/Hostname.pm in @INC
by Billah, Tashrif 09 Apr '25

09 Apr '25

We have always untarred up to 7.1.0 and used it successfully. This was the good thing about FreeSurfer that did not require a client side installation. I am the administrator and I can tell you that installation of this software via root is infeasible for 100 computers. Given your comment about 7.4.1 tarball being not installer, we want to know--has the installation mechanism changed since 7.4.1? Best, Tashrif

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