Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

what does the CSF label describe?
by Benjamin Luerweg 14 Sep '17

14 Sep '17

dear all, i already tried to find out what the label CSF stands for.. but beside realizing that its not a common/regular part of the ventricle system i couldn’t get any other informations regarding the meaning? of the CSF label. i tried to find out whats it about by using freeview (screenshot (black part)) anyone any idea? kind regards, b. luerweg doctoral student

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Re: [Freesurfer] lobes volume (WM and GM)
by Gonzalo Rojas Costa 14 Sep '17

14 Sep '17

Hi Douglas: By removing --rip-unknown I got the same results... Why ?... Sincerely, Gonzalo Rojas Costa > Date: Tue, 12 Sep 2017 12:33:11 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] lobes volume (WM and GM) > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <d547d519-c2fd-980d-3021-2c5fd44620a3(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Try removing the --rip-unknown > > > On 09/12/2017 11:09 AM, Gonzalo Rojas Costa wrote: >> Hi: >> >> I created the following script (for freesurfer 5.3.0) to compute the >> lobes volume (including GM and WM). >> >> mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos >> --seg lobulos --stat lobulos >> mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos >> --seg lobulos --stat lobulos >> mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh >> mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh >> mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown >> --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos >> --wmparc-dmax 20 >> mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab >> /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum >> $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 >> 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 >> >> But, I didn't got the complete WM volume for each lobe (frontal lobe >> for example... see red arrow in attached image)... why ?... Any >> solution ?... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> Laboratory for Advanced Medical Image Processing >> Department of Radiology >> Cl?nica las Condes >> Lo Fontecilla 441, Las Condes, Santiago, Chile. >> Tel: 56-2-2105170 >> Cel: 56-9-97771785 >> www.clc.cl >> http://www.aribrain.info >> https://scholar.google.com/citations?user=LO7LZ3oAAAAJ >> https://www.researchgate.net/profile/Gonzalo_Rojas2 >> https://cl.linkedin.com/in/gonzalorojascosta >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Cluster-Defining Threshold of p=0.025
by Douglas N Greve 14 Sep '17

14 Sep '17

Andy, please remember to post to the FS list, thanks. As for your question, this is a bug in mri_glmfit-sim that hard codes the allowable thresholds. I've attached a version that should work with 1.6. On 09/14/2017 10:06 AM, Jahn, Andrew wrote: > Thanks again; I was able to create new simulation tables. However, > when I run mri_glmfit-sim, I get the following error: > > foreach dir (results_Directory) > mri_glmfit-sim \ > --glmdir {$dir} \ > --mczsim 1.6 abs \ > --cwp 0.05 \ > --2spaces > end > > ERROR: thresh = 1.6, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > > I get this error even though I have the tables located in > $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/abs. > Is there something I'm missing? > > > Best, > > -Andy > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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mri_convert: line 3: 38445 Segmentation fault
by M Janani 14 Sep '17

14 Sep '17

Hi Team, Am getting segmentation error during the reconstruction process. Please help in resolving the error. I have attached log for reference. Thanks, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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correcting defect
by Meng Li 14 Sep '17

14 Sep '17

Hi all, I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half of the subjects was stuck at the ‘Correcting Defect’ step. However, when I changed to FreeSurfer version 5.3.0, the ‘Correcting defect’ step finished successfully. Is it possibility that the unsuccessful ‘Correcting Defect’ step is caused by the different versions of Freesurefer? In addition, when I added the flag -parallel -openmp 30 based on the version 6.0.0, the recon-all –all runtime still need 20+ hours. It seems that the parallel processing did not reduce the processing time. I wonder why the parallel processing did’t save time? Any help would be greatly appreciated. Meng

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Brain without skull and manual edits
by M del Mar Velasco 14 Sep '17

14 Sep '17

Dear all, I would like an accurate segmentation of the brain without skull in native space. I am running a recon-all with Freesurfer 6 and Ubuntu 16.04. When it finishes, I find mistakes and I erase some skull voxels from brainmask.mgz. I run recon-all again and it finished without errors. When I used to do that proccess with Freesurfer 5.1, I masked rawavg.mgz with brain.mgz to get the final segmented brain: mri_mask rawavg.mgz brain.mgz brainraw.mgz mri_convert -odt float brainraw.mgz brain.nii In that case, deleted voxels are set to background in brain.mgz (my manual changes affect to brain.mgz). Now I am using Freesurfer 6 and my manual erased voxels appears in brain.mgz (they are not black). So, what output from Freesurfer should I use to the above goal? Should I use brain.finalsurfs.mgz? Thanks you in advance M del Mar

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license error
by Ritesh Mahajan 14 Sep '17

14 Sep '17

Hello team, I created the license.txt at location FREESURFER_HOME and pasted the lines sent to me after registration. Still i find the following errors. "ERROR: FreeSurfer license file /usr/local/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment" Thanks, Ritesh Mahajan

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problems with segmentHA_T1_long.sh
by Lara Foland-Ross 13 Sep '17

13 Sep '17

Hello, I ran a longitudinal analysis cortical structure in Freesurfer version 5.3. I'd now like to compute hippocampus subfields using the new beta version of the "Segmentation of hippocampal subfields and nuclei of the amygdala" tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) I'm running into several errors when running segmentHA_T1_long.sh. Upon closer inspection of the script, it's not clear to me whether this tool is compatible with scans processed in the 5.3 version of the longitudinal pipeline. Can you please confirm? Thanks, Lara

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BA Labels
by John Anderson 13 Sep '17

13 Sep '17

Dear FS experts, I have SUV maps for subjects within two groups. I moved these SUV maps into surface then I concatenated the images in the order of two groups then I used the compiled file in a glm analysis to check the difference between the two groups. I aim to use V1 Atlas to derive the SUV values from the BA labels. I am not sure how to utilize these labels in such analysis. In this context I have two questions: 1. Can these label be converted to ROIs similar to the ROIs derived from wmpar.mgz using the command mri_binarize? 2. in WIKI it was mentioned that the command "recon-all -s subjid -label_v1" output the stat values for every BA label. How can I derive similar stats from the SUV maps in the compiled file. Thanks in advance John

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Unknown regions in cortical parcellation
by Aidan Murphy 13 Sep '17

13 Sep '17

We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the aparc volume we're noticing fairly large unknown regions in what should be entorhinal cortex, specifically where it comes up against the hippocampus and amygdala. The aseg volumes label these unknown regions as cortex. I've searched the archives and haven't been able to find anything similar from recent years. I've attached some axial screenshots of the raw T1, the aseg and the aparc+aseg.

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Freesurfer September 2017