Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Merging two groups
by Ramesh Babu 28 Nov '17

28 Nov '17

Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory or is there any others steps to merge? Thanks in advance RB

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medial wall label in Freesurfer 6
by Sofia Rodriguez Penuela 28 Nov '17

28 Nov '17

Hello, when using "make_average_subject" in Freesurfer 6, we have noted that the medial wall label only contains 1 vertex leading, after applying "mri_glmfit, to significant results in regions of the medial wall. This problem didn't appear in Fresurfer 5.3 Is there something different with the command "make_average_subject" in Freesurfer 6 that prevent to correctly mask the cortical surface? We would like to include only cortical vertices in our analysis. Thank you in advance. Best, Sofia -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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covariates in Qdec
by 박경일 28 Nov '17

28 Nov '17

Dear experts, I am trying to compare 2 groups with 2 covariates (age, sex) using qdec. After loading data, design tab displays "diagnosis" in discrete, "age" and "sex" in both continuous (covariates) and nuisance factor boxes. I just selected "diagnosis" and click "analyze". Is this a right way to remove effects by age and sex? Otherwise, do I need to check age and sex in nuisance factor box? Thank you so much. Park

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Recon-all -hires
by Hwee Ling Lee 28 Nov '17

28 Nov '17

Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling

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Re: [Freesurfer] make_average_subject label files
by M del Mar Velasco 28 Nov '17

28 Nov '17

I say I get only one vertex because lh or rh.Medial_wal.label has only one line. And lh or rh.cortex.label has 163841 lines. I send you the .label files that confirm it. I send you make_average log files too. Thanks you, M del Mar

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Skull-strip issues: commands not working
by Arsenije Subotic 27 Nov '17

27 Nov '17

Dear experts, I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command as the troubleshooting tutorial suggested to regenerate the surfaces based on the new brainmask.mgz volume: recon-all -autorecon-pial -subjid <subject name> However, after the subject finished processing the surfaces were generated/outlined on the dura as well. I tried performing a g-cut command but it did not get rid of the dura. I also had issues with the subcortical segmentation as the ventricles were not completely segmented. Thank you for your help. Best, Arsenije

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error in make_average_subject
by Duran, Tugce 27 Nov '17

27 Nov '17

Dear FreeSurfer Experts, I’m getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited with ERRORS at Wed Nov 15 19:14:17 EST 2017 It appears that during the process it doesn’t create the norm.mgz file to read or open it in the later processes (I think?). What can I do to fix this error? Thanks, Tugce

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Eklund's 2016 and FreeSurfer
by Sahil Bajaj 27 Nov '17

27 Nov '17

Hi, I was wondering if there is any paper published by FreeSurfer team or FreeSurfer experts (after Eklund's 2016 paper) stating that the cluster failure issue is not an issue in FreeSurfer toolbox and/or whether CFT of less than 0.05 or 0.01 to estimate cortical thickness/volume/area maps is fine to use if Monte-Carlo simulations (MCZ) in FreeSurfer. I am looking for any such paper to cite in one of my papers I am working on. Thanks ! Sahil

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make_average_subject label files
by M del Mar Velasco 27 Nov '17

27 Nov '17

Dear Freesurfer experts, I have a question related to make_average_subject command and Freesurfer versions. When I used to create my average subject with Freesurfer 5.3, I got lh.cortex.label and rh.cortex.label files inside label folder with 149955 vertexs. Moreover, lh.Medial_Wall.label and rh.Medial_Wall.label had 13887 vertexs. However, with new Freesurfer 6, I get 163841 vertexs for cortex and only one vertex for medial wall. That's why I have problems with mri_glmfit when I use rh or lh.cortex.label files as label mask. I am considering all vertexs, and I would like to use only real cortex vertexs. Are label files outputs from make_average_subject wrong? How can I fit this problem? Thanks in advance, M del Mar

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Back to native space after registration
by Avideh Gharehgazlou 27 Nov '17

27 Nov '17

Hi experts, Will you please briefly explain to me the rationale behind why subjects put back into their original space after alignment to the template (fsaverage)? and also, how this is done. Thanks so much, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Freesurfer November 2017