Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Freesurfer troubleshooting for ageing data
by Niklas Kasenburg 06 Oct '14

06 Oct '14

Hello fellow Freesurfer user, I am currently working on an ageing data set (~60 subjects between 19 to 81 years old). I mainly want to use Freesurfer for two different things: 1. get a cortical and sub-cortical segmentation to use those regions for a connectivity analysis 2. use the WM/GM boundary and the pial surface to compute cortical thickness I have run recon-all -autorecon2 for all subjects based on T1-weighted structural images. I am no in the process of making sure that everything worked before continuing (I already checked after autorecon-1 that the skull striping didn't remove large chunks of the brain). Therefore, I looked at the surfaces and saw that there are problems with almost half of my subjects due to bad skull striping (WM/GM boundary or pial surface extends to skull). I also read that lesions (WM surface cutting into the brain instead of following it) can lead to dimples or holes in the inflated surfaces. I know that one can correct some of those errors manually, but probably not all the errors will have an impact on what I want to use it for. Which brings me to the questions: 1. Which parts are critical for my subsequent analysis (concerning points 1 and 2 above) and therefore need to be corrected? 2. How much time should you generally invest on manual intervention (erasing voxels in brainmask.mgz, filling holes in wm.mgz, etc.) and when should you rather refine parameters in the recon-all processes (see also 3)? 3. If there are a lot of errors due to wrong skull stripping, how can you change steps in the pipeline to improve it? I would really appreciate help with any of the three points, so feel free to just answer to a subset of them. Many thanks in advance! Best regards, Niklas

1 0

excluding labels from analysis
by Adam, Ruth 06 Oct '14

06 Oct '14

1 0

Any ideas on how to automatically measure maximum thickness(diameter) of lesions?
by 조수연 06 Oct '14

06 Oct '14

Hello, dear fellow Freesurfers. I was wondering whether there was any way to automatically measure the longest or the maximum length(or thickness or diameter) of cortical lesions. By this I mean that if there were to say 3 distinctive lesions in the brain of the patient, each with 1mm, 2mm, 7mm maximum diameters, the 7mm will be chosen as the representative "maximum lesion thickness" of the patient. Considering that there are automated methods to measure the average cortical thickness, with a little tweaking, it seems plausible that we can measure the lesion's maximum thickness automatically too. I know there are provided methods that able us to automatically segregate lesion specific areas from T1 FLAIR images. Will there be a way to get the measurements that I want using these masks? Using the masks isn't essential as long as I can get the maximum lesion thickness automatically. I'm not so familiar with computational algorithms so please any form of advice will be appreciated. Thank you for taking your time to read this. Hope all of you have a great day. Sincerely, Sooyun Cho.

2 1

Re: [Freesurfer] White matter and white matter lesions
by Douglas N Greve 06 Oct '14

06 Oct '14

Those are the only WM labels present in the aseg. You may or may not want to include brain stem as WM. On 10/03/2014 04:03 AM, Leise Borg wrote: > > Hi again > > Labels 7 and 46 in the aseg-file gives me the cerebellum white matter > – which I can see from the aseg.stat-file. From the list at > http://www.slicer.org/slicerWiki/index.php/Slicer3:Freesurfer_labels I > can see that I also need the labels 2 and 41. It looks ok to me when I > plot it, but can I be sure that it gives me all white matter (NOT > white matter hypointensities)? I can see that there are several other > labels referring to white matter, such as label 219, 223, 3000 etc. Do > those labels point at subsets of the labels 2 and 41 (and 7 and 46)? > > -Leise > > *From:*Leise Borg > *Sent:* 3. oktober 2014 08:48 > *To:* 'greve(a)nmr.mgh.harvard.edu' > *Subject:* Re: [Freesurfer] White matter and white matter lesions > > Hi Douglas > > Thanks a lot for your answer. I will definitely do that. Can you tell > me how I load this aseg.stats file into Matlab? I do not have > FreeSurfer downloaded on my own computer. Do I need that to load this > file? > > -Leise. > > Why not just use the values in aseg.stats? > > On 10/01/2014 07:44 AM, Leise Borg wrote: > > > > > > Hi FreeSurfer > > > > > > I am working on a project concerning Alzheimer’s patients and I need > > > to know the positions of white matter (WM) and white matter lesions > > > (WML) from your segmentations. > > > > > > To find the WML, I use label 77 in the aparc.a2009s+aseg.mgz-files. > > > > > > To find the WM, I use labels 2 and 41 in the ribbon.mgz-files and > > > subtract the ventricles by subtracting labels: 4, 5 14, 15, 43 44 > > > found in the aseg.mgz-files. > > > > > > However, in the two sets of positions – one for WML and one for WM > > > –there is an overlap. It is not big, but it is there. > > > > > > Can you help me finding the true WML- and WM-segmentations? > > > > > > With kind regards, Leise. > -- 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/

4 4

PhD position in tractography validation, Inserm U930 "Brain and imaging" lab, University François-Rabelais of Tours
by Frédéric Andersson 06 Oct '14

06 Oct '14

"A funded PhD Student position will be available in the “Brain and Imaging” Inserm unit (national institute for health) settled in Tours, France, from October 1st, 2014 to September 30th, 2017. During this time period, the candidate will have: (1) to develop tools and pertinent criteria for comparison of MR-based tractography results to data obtained from dissection; (2) to compare different algorithms used for MR-based tractography; (3) to develop a tool aiming to help decision making for the choice of optimal algorithms and parameters used for tractography. This work will be co-directed by Pr C Destrieux (Anatomist) and Pr G Venturini (Computer Science) in the university of Tours. It will be funded for the whole time period by a grant we obtained from the Ministry of Research (about 1400 € per month). Potential candidates have to send a letter and a CV to christophe.destrieux(a)univ-tours.fr and gilles.venturini(a)univ-tours.fr before the 15th of April. After an internal selection of the applications, they will have to defend their candidateship during an interview organized by the Doctoral School of the university at the end of May 2014."

1 1

Transform MNI-space segmentation into Subject-space
by Roy Talman 06 Oct '14

06 Oct '14

Hello I have a segmentation which made on MNI space, is it possible to do the inverse transform to the segmentation from MNI space to each subject space? does the size of the MNI segmentation (218*182*182) should be a problam? I was traing : mri_vol2surf MNI_Segmentation.nii --hemi lh --regheader bert --o /home/cnilab/ProgramFiles/freesurfer/NewFileName.mgz but i get a empty file. is there a diffrante way to do this? thanks. roy

2 2

rawfunc2surf-sess with a limited set of surface files
by Reza Rajimehr 05 Oct '14

05 Oct '14

Hi, I want to use rawfunc2surf-sess to project the functional data onto the surface in the source subject and then in the target subject. My source subject has been processed in Freesurfer. However, my target subject has been processed in Caret, so I do not have all the surface files for the target subject. To get rawfunc2surf-sess to work for my situation, I have to make some minor changes in its code. By looking at the code, I realized that rawfunc2surf-sess calls mri_vol2surf for mask and raw data, then it calls mris_fwhm to smooth raw data within mask. I am describing the changes that I have to make in these two commands, plus a specific question for each change: 1) mri_vol2surf includes the --cortex flag. Since I do not have cortex.label in the target subject, I am removing this flag. Would this be problematic later on? I will eventually do specific analyses on the occipito-temporal vertices in Matlab. Since I have lobar labels in the target subject, I can select/mask those vertices later on. 2) For the source subject, I have the white and pial surfaces. For the target subject, I have the midthickness surface which is somewhere between white and pial. I am adding --surf midthickness in mri_vol2surf to specify the target surface to be midthickness (instead of white). Will this be a problem when the source subject does not have such surface? 3) There is --projfrac 0.5 in mri_vol2surf. The help says "When [the projfrac is] set at 0.5 with the white surface, this should sample in the middle of the cortical surface. This requires that a ?h.thickness file exist for the source subject". I have the thickness file in the source subject - though I don't have it in the target subject. Does 'projfracing' happen only for the source subject? 4) I assume that mris_fwhm will work fine for my situation, unless it requires the white surface in the target subject. Which file is used in mris_fwhm for extracting the vertices coordinates? Thanks in advance for your advice, Reza

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 127, Issue 37
by Nikita Zhitkevich 04 Oct '14

04 Oct '14

Hi Bruce, I'm running Ubuntu version 14.04 LTS and Freesurfer version 1.379.2.65. I am only trying to run the Bert test lines when I come up with the segfault error I mentioned earlier so command line : tkmedit bert orig.mgz which comes up with ERROR: A segfault has occurred. This is not your fault, but is most likely an unrecoverable error and has made the program unstable. Please send the contents of the file .xdebug_tkmedit that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu. which is the only message displayed at that point. Any suggestions? Nikita Zhitkevich > From: freesurfer-request(a)nmr.mgh.harvard.edu > Subject: Freesurfer Digest, Vol 127, Issue 37 > To: freesurfer(a)nmr.mgh.harvard.edu > Date: Wed, 24 Sep 2014 12:00:02 -0400 > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > 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. longitudinal analysis and linear mixed effects models > (Emma Thompson) > 2. Re: Pial Surface Incorrect For Native T1 (Zachary Greenberg) > 3. Segfault Error (Nikita Zhitkevich) > 4. how to extract the individual cortical thickness or volume > value of significant cluster after RFT correction (wang kangcheng) > 5. Re: how to extract the individual cortical thickness or > volume value of significant cluster after RFT correction > (wang kangcheng) > 6. Re: Segfault Error (Bruce Fischl) > 7. Re: longitudinal analysis and linear mixed effects models > (Martin Reuter) > 8. Re: Vertex wise analysis and area/pial area/volume > interpretation (Las Blawimo) > 9. Brainhack Eastern Standard Time - Boston October 18-19, 2014 > (MCLAREN, Donald) > 10. watershed problem (Anastasia Klimovich-Smith) > 11. Re: how to extract the individual cortical thickness or > volume value of significant cluster after RFT correction > (Douglas N Greve) > 12. Re: Pial Surface Incorrect For Native T1 (Douglas N Greve) > 13. Re: Scatter plot from mri_glmfit analyses (Douglas N Greve) > 14. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Douglas N Greve) > 15. Re: Volume to surface coordinates (Douglas N Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 23 Sep 2014 17:55:27 -0400 > From: Emma Thompson <voneconomos(a)gmail.com> > Subject: [Freesurfer] longitudinal analysis and linear mixed effects > models > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+BXJQJHWhSi2p+Yr25Cb_yUxcb-hEwPwCbdtV96Y=ub+Qh_8A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi FS, > I want to conduct a within-subjects longitudinal analysis, I thought I > would be able to run a LME model in QDEC but this doesn't seem to be the > case at all, is this correct? It seems I have to do everything using Matlab > (big sigh). > > https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > > > I have already preprocessed the data: 1) cross for all time points, 2) > base, and then 3) long according to the awesome tutorial provided by FS. > > I have only one group, a patient population that was scanned prior to > (bseline) and at various time points (3 time points post) following > treatment. Would you agree that the best analytical approach for me would > be the LME model, especially since I have a few subjects with a couple of > missing post-treatment time points? > > Is there any way you would recommend another approach using QDEC? > > Lastly, I have done everything in FS version 5.1, I'm considering upgrading > to 5.3, since my freeview software seems to be out of date. It also seems > that the Matlab tools I need to run LME are only available in FS version > 5.2. At this point a little concerned since I'm hoping I didn't waste a > bunch of time just realizing all this now, would upgrading to 5.3 > negatively impact all the work I've done thus far using version 5.1? > > Thanks for the help!! >

1 0

Re: [Freesurfer] A question about spherical registration
by Reza Rajimehr 04 Oct '14

04 Oct '14

Hi Doug, Before I saw your response, I modified make_average_surface code by removing -annot aparc flag in the mris_make_template command within this code, and my script worked fine all the way to the end without any error. The change you made in make_average_surface would be useful in future. Just a minor point: You have modified this part: set cmd = (mris_make_template -norot aparc \ $hemi $sphere_reg $SUBJECTS $atlas) if($UseAnnot) set cmd = ($cmd -annot) Not sure if aparc should be kept in the line ... Best, Reza It is trying to use the annotation when making the registration tif. This is hard coded in your version of make_average_surface. I've attached a new version. Run it with --no-annot. Let me know if it works and I'll check it into our distribution doug

1 0

R: Re: mri_binarize error
by stdp82＠virgilio.it 03 Oct '14

03 Oct '14

My apologies the error is in the pathway. I did not add /mri to /Applications/freesurfer/subjects/Control20 Regards, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 3-ott-2014 22.03 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mri_binarize error does that file exist and do you have read permissions? On 10/03/2014 04:02 PM, stdp82(a)virgilio.it wrote: > Hi list > > I'm running > > mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 1029 1031 > --o lh.parietal.nii.gz > > and I get this error: > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /Applications/freesurfer/subjects/Control20 > cmdline mri_binarize --i aparc+aseg.mgz --match 1005 1008 1010 1025 > 1029 1031 --o lh.parietal.nii.gz > sysname Darwin > hostname iMac-di-Stefano.local > machine x86_64 > user Stefano > > input aparc+aseg.mgz > frame 0 > nErode3d 0 > nErode2d 0 > output lh.parietal.nii.gz > Binarizing based on matching values > nMatch 6 > 0 1005 > 1 1008 > 2 1010 > 3 1025 > 4 1029 > 5 1031 > binval 1 > binvalnot 0 > mghRead(/Applications/freesurfer/subjects//Control20/aparc+aseg.mgz, > -1): could not open file > > Thanks > > Regards, > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer