Freesurfer

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Questions related to combining datasets run through different versions
by Lisanne Michelle Jenkins 24 Feb '21

24 Feb '21

External Email - Use Caution Hi experts, We want to combine two large datasets (of patients with different diseases) that have been processed and manually edited using Freesurfer 5.3 and Freesurfer 6.0. From the Freesurfer website and previous posts, we have read that we should re-run the Freesurfer 5.3 data that has been manually edited (both brain masks and pial surfaces) through Freesurfer 6.0 using recon-all and using the -continued flag, and that the manual edits from 5.3 should carry over. However, we have found that around one-third of subjects have skull stripping errors after rerunning through 6.0. Has anyone else found this? Have we missed something? A related question: We have heard it argued that if the data has been manually edited and quality checked, the version of Freesurfer which it is run through should not matter, therefore it is ok to combine data from different versions – what do you think of this argument? An additional argument along those lines that we have heard is: If one were to re-process data with a later version of Freesurfer, using edits from an older version would introduce biases from that version – what are your thoughts on this argument? Thank you. Lisanne

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segmentation is shifted with respect to NIFTI T1W
by Roman Fleysher 24 Feb '21

24 Feb '21

External Email - Use Caution Dear FreeSurfers, I am working with version 6, starting point is T1W image in NIFTI format. I typically transform segmentations back to native space in NIFTI format to be able to use other software (FSL and such). I noticed that segmentation is shifted by 1 pixel in one axis (y-axis). Mapping of segmentation is a two step process based on description in: http://secure-web.cisco.com/1OQ80xn8YGeWjUO2KyO4RDGDpL87LZ0EBpX6Z7_yDHTAQnU… Specific commands are (schematically) : # realign to original MGZ mri_label2vol --seg inputSegmentationInMGZ --temp mri/orig/001.mgz --o outputSegmentationInOrigMGZ --regheader inputSegmentationInMGZ # convert to NIFTI (*.nii.gz) mri_convert --in_type mgz --out_type nii outputSegmentationInOrigMGZ outputSegmentationInOrigNIFTI.nii.gz Are these steps correct? I can shift NIFTI by one pixel using fslroi, but I want to be sure nothing else is happening and that this shift is the correct work around. Thank you, Roman

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rerunning FS 7.1.1 after brainmask.mgz edits
by Alexopoulos, Dimitrios 24 Feb '21

24 Feb '21

External Email - Use Caution Hi, We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the "cloning to T1 method", using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz. Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline? We originally ran: recon-all -s -i -hires -all Do we run the same command again or should we use: recon-all -s -make -hires all Thanks. Jim ________________________________ 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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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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