Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

must specify a subject id
by 况况 24 Feb '21

24 Feb '21

External Email - Use Caution hello i downloaded dev version, input FREESURFER_HOME=/home/siying/sharefolder/freesurfer-linux-ubuntu18_x86_64-dev/freesurfer export SUBJECTS_DIR=/home/siying/sharefolder/freesurfer-linux-ubuntu18_x86_64-dev/freesurfer/kuang_dev/kuang_dev_results source $FREESURFER_HOME/SetUpFreeSurfer.sh then run recon-all -s ch2 -i /home/siying/sharefolder/freesurfer-linux-ubuntu18_x86_64-dev/freesurfer/kuang_dev/kuang_dev_data/ch2/ch2.nii -all –qcache -parallel , then and appeared 'ERROR: must specify a subject id', what should i do to solve it?

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Hippocampus subfiled segmantation addtional scan
by Wei Shao 23 Feb '21

23 Feb '21

External Email - Use Caution Hi, Freesurfer experts I used the Freesurfer7.1.0 version for the hippocampus subfield segmentation, and I use a coronal T2 scan as an additional to do the segmentation . [image: 14352.PNG] I'm wondering that the reason for the two black blocks in the sagittal and axial view is because I only use the coronal T2 anat scan for the additional scan? Can I add another axial scan for the T2 subfield segmentation without deleting anything (like hippocampal-subfields-T2.T2.log)? Thanks Best, Wei

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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?
by Gronow, Franziska 23 Feb '21

23 Feb '21

External Email - Use Caution Dear Eugenio, thank you for your response. Unfortunately it is not possible to share the whole subject. Would it be helpful to send you more screenshots of all three views (coronal, sagittal, axial) with different mask opacities? Kind regards, Franziska -----Ursprüngliche Nachricht----- Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> Im Auftrag von freesurfer-request(a)nmr.mgh.harvard.edu Gesendet: Mittwoch, 17. Februar 2021 14:56 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 204, Issue 33 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1ak9QaJ1_1rhd69MSCjVvSgBkkgvkfHMc4AJu1OKXYs9k4… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: overlap/intersection of labels? (Trisanna Sprung-Much) 2. Re: FreeSurfer 7 vs FreeSurfer 6 surface differences (Mike Schmidt) 3. VB password (?????????) 4. Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Gronow, Franziska) 5. Queries in qdec (Koustav Chatterjee) 6. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.) 7. Re: Thalamic nuclei segmentation - PuM nucleus mis-segmentation? (Iglesias Gonzalez, Juan E.) ---------------------------------------------------------------------- Message: 1 Date: Tue, 16 Feb 2021 21:58:34 +0000 From: Trisanna Sprung-Much <trisanna.sprung-much(a)mail.mcgill.ca> Subject: Re: [Freesurfer] overlap/intersection of labels? To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D5D39FEB-2D09-4051-B15C-49E61BFB8B61(a)mail.mcgill.ca> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Cornelius I found something that computes the overlap of labels across the same vertex when doing some research about this, not sure if this is what you mean: https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4… See specifically: --nhits <nhits_file> This option creates a diagnostic file showing whether the cumulative effect of all the label files happens to assign more than one label to each vertex. The output file is a FreeSurfer<https://secure-web.cisco.com/1QIgJhgEjv5N9NM6Uh6927wVezy6eduY2p7_2aAiUh0J8f…> 'overlay' format file, in which each vertex has an associated value, in this case the count of labels assigned to that vertex. This can be displayed in tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices (count<=1) from bad (count>=2). I know there is also a command merge_labels that may help? Best, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre -- From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Dr. Cornelius Kronlage" <Cornelius.Kronlage(a)med.uni-tuebingen.de> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, February 16, 2021 at 11:19 AM To: "'freesurfer(a)nmr.mgh.harvard.edu'" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] overlap/intersection of labels? External Email - Use Caution Dear freesurfers, is there an elegant way of computing the intersection or overlap of different labels or - which would be even more useful for my application - annotations? I only managed to find labels_intersect (which appears to be from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16WQ5tQQPY74lwcUD6e-u4HAYMeACJcAQ4y9i44WDTIAnw…<https://secure-web.cisco.com/12D3ntbm8RDBV366hh41UjEkFWk2mrjQHSMiY8WEom0naU…> ) which is awfully slow. In case this is of use for anyone else, I att ached a modified version using 'join' that runs much faster, only has some compatibility issues with Mac. >time labels_intersect precentral.label frontal.label out1.label > >/dev/null real 1m41.862s user 0m31.052s sys 0m30.757s >time bash bash_labels_intersect.sh precentral.label frontal.label >out2.label real 0m0.193s user 0m0.118s sys 0m0.015s >diff -w out1.label out2.label > Thank you and best wishes Cornelius -- Cornelius Kronlage Assistenzarzt Klinik f?r Neurologie | Neurologie mit Schwerpunkt Epileptologie Universit?tsklinikum T?bingen Hoppe-Seyler-Str. 3 | 72076 T?bingen

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problems about freesurfer7 with T2pial flag
by Yijun Chen 23 Feb '21

23 Feb '21

External Email - Use Caution Hi freesurfer experts: I encountered a problem about freesurfer 7 with the T2pial flag. when I use the freesurfer 6 — recon-all -all -i -s -T2 -T2pial, the resulting T2.mgz is skull-stripped. however, when I switch to the freesurfer 7, the resulting T2.mgz is with skull. Is there anything wrong? Thanks, Yijun.

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FDR correction for statistical maps in Freeview?
by Hannah Eichhorn 23 Feb '21

23 Feb '21

External Email - Use Caution Dear all, I am using glmfit to analyse changes in cortical thickness, but I couldn't find a description on how to perform FDR correction with FreeSurfer. Is there a way to perform FDR correction of the statistical maps in Freeview, analogous to how it is described for tksurfer in this tutorial: https://secure-web.cisco.com/1znvz_BL1QGomjuCvGB8n8AR_x-UOEpT7dpaUNIadO4EOr… Thank you very much for your help! Best regards, Hannah

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Question about statistical data for cerebellar segmentation ?
by Viktor-Jan De Deken 23 Feb '21

23 Feb '21

External Email - Use Caution Hi Freesurfer I would like to perform statistical analesys on cerebellar segmentation data. For my purposes, The atlases that come with Freesurfer don't give enough parcellation of the cerebellum. I tried looking online and found this email conversation: https://secure-web.cisco.com/1229EcuHvdmZnZf2i3VnPduj5r7wBNepLb6mPJVJg1F2on… I applied this and it worked visually but I want statistical data like in the aseg.stats or aparc.stats files. Can you help me? Kind regards Viktor-Jan

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recon-all error: No such file or directory
by Eduardo Bergonzoni Junqueira 23 Feb '21

23 Feb '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to preprocesss a t1.nii.gz image in freesurfer with recon-all. I'm following the tutorial for linux in https://secure-web.cisco.com/1LNJqjy9_CcjRF6N2vjvepp4rKUty6HrwT4CmaUGa6hhi_…. (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export FREESURFER_HOME=/usr/local/freesurfer (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /home/eduardo/fsl I'm getting the following error when I run the command: (base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ recon-all -s Grant_sub -i t1.nii.gz -all ERROR: /home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or directory. This error is strange for me. I don't know why it is showing "\301rea de Trabalho/" if the correct name of the directory is "Área de Trabalho". The t1.nii.gz is in the path directory I'm using in the terminal. Please, can anybody help how to fix this bug? I've looked for similar bug reports. Probably it is something simple, but I couln't found how to solve the problem. 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu 20.04.1 3) uname -a: Linux eduardo-X555UB 5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri Feb 5 09:57:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Best regards

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Brain normalisation to intracranial volume
by Carolina Rimkus 23 Feb '21

23 Feb '21

External Email - Use Caution I would like to know which are the best ways to normalize the VOI's to intracranial volume. Also, what is the variable BrainSegVol-to-eTIV in aseg? Is it a scaling factor? Does freesurfer segmentation provide a scaling factor? Best regards, Carolina -- Carolina M Rimkus, MD, PhD Neuroradiologist Department of Radiology, Faculty of Medicine, University of São Paulo-SP, Brazil email: carolina.rimkus(a)usp.br carolina.rimkus(a)gmail.com

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Drawing labels on flat patch.
by Devavrat Vartak 22 Feb '21

22 Feb '21

External Email - Use Caution Hello freesurfer experts, Freeview v3.0 FS 7.1.1 I am able to draw labels on the 3D surface and display it on a flat patch, but when I try to draw directly on the flat patch it keeps drawing in the 3D-space. Is it possible to draw labels on the flat patch directly ? Thank you. Cheers, Dev

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Application for Chinese Postdoctoral Scholarship on Dynamic Brain Connectivity
by Joana Braga Pereira 22 Feb '21

22 Feb '21

External Email - Use Caution Dear all, If you have earned a PhD degree in China in the last 3 years and would like to do a Postdoc at Karolinska Institute in Sweden, please see the project below: *Dynamic Changes in Functional Brain Connectivity over the course of Alzheimer’s Disease* The aim of this project is to apply new methods that analyse brain connectivity as a highly dynamic process across different stages of AD. This will be performed by combining resting state functional magnetic resonance imaging with graph theory methods in different cohorts of patients and healthy controls. Once the dynamic brain network changes have been identified, their relationship with CSF biomarkers and cognitive function will be assessed. In addition, it will also be possible to apply machine-learning algorithms in this project as well as combine the data with anatomical brain connectivity measures derived from diffusion tensor imaging. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, engineering, physics, medicine, statistics, neuropsychology or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with functional magnetic resonance imaging, diffusion tensor imaging, positron emission tomography or other neuroimaging techniques; - Clinical or research experience with aging and/or neurodegenerative disorders; - Good writing and communication skills in English; - Good record of scientific publications. If you are interested in applying for a scholarship, please send an email with your CV to *joana.pereira(a)ki.se <joana.pereira(a)ki.se> *as soon as possible. Best wishes, Joana

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