Freesurfer

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30132 discussions

control point and aseg edit
by miracle ozzoude 14 Sep '17

14 Sep '17

I used the expert option for control points and manually edited the aseg.presurf.mgz. Which is the proper flag to use in other to incorporate the respective changes? a) recon-all -autorecon2-cp -autorecon2-noaseg -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time or b) recon-all -autorecon2-cp -autorecon3 -expert -parallel -openmp 8 -bigventricles -3T -time Thanks. Best, Paul

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Using FreeSurfer5.3 via VirtualBox
by Ledesma, Jason 14 Sep '17

14 Sep '17

To whom it may concern, How does one access the files in a shared folder when using FreeSurfer5.3 via VirtualBox on a windows unit? I have not had success with the "sudo mount -t vboxsf <shared_folder_name> /media/<shared_folder_name>" command which I have seen on several forums. Furthermore, I continually receive a warning which states that the "...VirtualBox Guest Additions do not appear to be available on this virtual machine, and shared folders cannot be used with them...", however I have inserted the Guest Additions CD image from the devices menu as the warning requests. Thanks. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ________________________________ LA BioMed Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ________________________________

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adding volumes of seperated parts of one structure?
by Benjamin Luerweg 14 Sep '17

14 Sep '17

dear all, what do you think about adding the volumes of seperated parts of one structure to a complete volume? e.g. the corpus callosum or also cingulate gyrus. is it ok to get the complete volume value by just adding the volumes of the seperated parts? beside that, am i right that wmparc parts of e.g. insula is just the white matter volume? would it be ok to add the volume of the aparc equivalent as the grey matter volume part? kind regards, ben luerweg

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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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