Freesurfer

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30084 discussions

Re: [Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0)
by Greve, Douglas N.,Ph.D. 28 Jan '20

28 Jan '20

Not sure, we have not been using that flag in a while. When you look at the volume in freeview, you can see what the code is by clicking on a voxel. You can change the offset by including --base-offset XXX to mri_aparc2aseg, On 1/24/2020 2:40 PM, Grodin, Erica wrote: External Email - Use Caution Hi Doug, Thanks for your reply. I ran the mris_ca_label command manually using the lh.atlas2005_simple.gcs and rh atlas. I then ran the mri_aparc2aseg with the --a2005s flag, which gives me an aparc.a2005s image. However, when I try to extract the VOIs that I need from that image I end up with an empty file and when I look at the aparc.a2005s image, the intensities only seem to go up to the 2000's instead of the 9000's which is what I need for the VOIs. I'm wondering if I am using the wrong .gcs file, but the simple 2005 one is the only one that seems appropriate. Thanks for your help! Erica ---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> Sent: Thursday, January 16, 2020 3:40 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0) I don't think so, but you can run mris_ca_label by hand. Look in the recon-all.log file for the command, then use the 2005 tif instead of the 2009 tif. I think it should work. On 1/16/2020 3:31 PM, Grodin, Erica wrote: External Email - Use Caution Hello, I am running recon-all on my data using freesurfer 6.0 which is working correctly. However, I need to create some VOIs which labels are only outputted from the aparc2005 set and do not appear in the aparc2009 set; specifically: 9001, 9501 ctx-lh-primary-motor, ctx-rh-primary-motor 9005, 9505 ctx-lh-prim-sec-somatosensory, ctx-rh- prim-sec-somatosensory 9002, 9502 ctx-lh-premotor, ctx-rh-premotor 9004, 9504 ctx-lh-posterior-parietal, ctx-rh-posterior-parietal Is there a flag or some other option to output the 2005 set in addition to the 2009? Thank you for your help, Erica Grodin ---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon exited with errors
by Desel, Tenzin 28 Jan '20

28 Jan '20

Hello FreeSurfer Developers, I'm attempting to run recon-all after unpacking data. It is exiting with errors - mri_cc: no WM voxels found with norm > 40 -- check skull stripping I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb 2) Platform: centos7_x86_64 3) uname -a: Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you!

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Reconstruction editing
by Jane Tseng 28 Jan '20

28 Jan '20

External Email - Use Caution Dear Freesurfer experts, I would like to ask for some advice about reconstruction editing. We have a subject that doesn't have great image quality, but we would like to try our best to make the data usable. One issue that we have is the pial surface is not capturing all of the gray matter (i.e. some gyri get cut out). I have tried adding control points and it improved in some regions but not all. Below are some examples, the light blue contour is the original pial surface and the red contour is the edited pial surface, the yellow contour is the edited white matter surface. Are there any suggestions on what else can be done? Just wanted to make sure that we've looked into all the options. Thank you!! Best wishes,Jane

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Recommendation for CFT and CWT FreeSurfer analysis
by Martin Juneja 28 Jan '20

28 Jan '20

External Email - Use Caution Hi, I am using Monte-Carlo simulations (for cortical thickness and volume - behavioral analysis) for clusterwise correction for multiple comparisons. My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e., CWT = 0.07) (smoothing 12 mm) for cortical thickness-behavior analysis - with maxima at -4.3 (CFT) or (ii) CFT < 0.05 and CWT < 0.001 (i.e., CWT = 0.0002) (smoothing 10 mm) for cortical volume-behavior - with maxima at -4.53 (CFT) Both the clusters in (i) (lateral orbital frontal) and (ii) (rostral middle) are within the frontal cortex, but not overlapping ! Also, although maxima is at (i) -4.3 and (ii) -4.53, still the clusters do not survive recommended thresholds suggested in https://www.ncbi.nlm.nih.gov/pubmed/29288131 And the FPR in this paper at strong CWT (i..e, 0.001) and liberal CFT (i..e, 0.05) is not calculated. So I was wondering if there is any recommendation from the experts regarding these results, or none of these make sense because I never get CFT < 0.001 and CWT < 0.05 (at-least). Any help would be really appreciated.

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dwi to native transformation
by Sam W 27 Jan '20

27 Jan '20

External Email - Use Caution Hello! I'm trying to create an fsl reg file that maps a dwi image to native anatomical space. 1. I used bbregister to create a reg file that maps the transformation from nodif to freesurfer's conformed space: bbregister --s sub001 --mov nodif.nii.gz --reg nodif2orig.dat --dti --init-fsl --fslmat nodif2orig.mat 2. then I aligned my dwi images to orig.mgz using the reg file from step 1 mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o dwi-in-freesurfer.nii 3. finally I mapped dwi-in-freesurfer image to native anatomical space mri_vol2vol --target mri/rawavg.mgz --regheader --mov dwi-in-freesurfer.nii --o dwi-in-rawavg.nii However I only get the registration file nodif2orig.mat, which only maps the nodif to freesurfer space? How can I get an fsl.mat for the transformation from freesurfer to native space? mri_vol2vol has no flag to output an fsl-type registration file. Best regards, Sam

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Calculate thickness in a ROI volume
by Larrabee, Matthew 27 Jan '20

27 Jan '20

Hi Karel, These are the commands we would run to calculate thickness in an ROI volume: mri_vol2surf mri_vol2label (please ignore misleading name, will also work on surfaces) mris_anatomicalstats The wiki has documentation on all of these programs, but if you would like further details feel free to reach out! https://surfer.nmr.mgh.harvard.edu/fswiki -Matt

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Retinotopy, design ill-conditioned
by Marco Ninghetto 27 Jan '20

27 Jan '20

External Email - Use Caution Hello experts, I'm performing retinotopy analysis but when running the command selxavg3-sess It starts, but after some lines, I get the following error: ERROR: design is ill-conditioned I don't know how to proceed from here to solve the error. My retinotopy stimuli make 2 cycles (e.g.: rotating wedge makes 2 full cycles before quit) and each cycle takes 200 seconds to complete. TR is set to 2.5 seconds. Please, does anyone have any advice? Thanks in advance, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Desikan and Destrieux Atlas information
by MOREAU Louise 27 Jan '20

27 Jan '20

External Email - Use Caution Hello, I am a user of recon-all and I was wondering if I could have more information on the .gcs files for the Desikan and Destrieux Atlas: · What are the different information stored in this file ? · Is the information stored on a surface or on a 3D volume ? If it is a surface, is the surface a sphere ? · Is there any information that can be extracted and read from those files ? · Is there any viewer of the files ? · In which coordinate system is the atlas ? Furthermore, I have a question about the FreeSurfer Coordinate System: · Why is there a need to change the Coordinate System ? Thank you in advance for your time and your answer, Best Regards, Louise Moreau This email and any attachments are intended solely for the use of the individual or entity to whom it is addressed and may be confidential and/or privileged. If you are not one of the named recipients or have received this email in error, (i) you should not read, disclose, or copy it, (ii) please notify sender of your receipt by reply email and delete this email and all attachments, (iii) Dassault Systèmes does not accept or assume any liability or responsibility for any use of or reliance on this email. Please be informed that your personal data are processed according to our data privacy policy as described on our website. Should you have any questions related to personal data protection, please contact 3DS Data Protection Officer at 3DS.compliance-privacy(a)3ds.com<mailto:3DS.compliance-privacy@3ds.com> For other languages, go to https://www.3ds.com/terms/email-disclaimer

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Re: [Freesurfer] Version 6.0 patches for hi-res data
by Alexopoulos, Dimitrios 25 Jan '20

25 Jan '20

External Email - Use Caution Ok. But the updated patches will need to be applied to the data generated with the -hires flag? Jim On Jan 24, 2020 5:32 PM, "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> wrote: For the -conf2hires, there is no problem because the segmentation is done at 1mm. On 1/24/2020 5:17 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution I came across info for version 6.0 that generated statistical errors when using high resolution input. https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed We have used the ‘-hires’ flag and, more recently, the ‘-conf2hires’ flag with recon-all.v6.hires command. Our input data is 0.8mm^3 I presume we only need to rerun the stats using the mri_segstats and mris_anatomical_stats patches, correct? 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ 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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Re: [Freesurfer] help: fs-fast group level analysis per run
by Rami Hamati 25 Jan '20

25 Jan '20

External Email - Use Caution Sorry if my question was unclear. We would like to analyze each run separately to observe if there is any habituation between runs of our task. Is there a way to concatenate each run separately? > Message: 15 > Date: Fri, 24 Jan 2020 15:36:36 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] help: fs-fast group level analysis per run > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <a30ff7c6-3179-7c73-54f1-636ff15d8bf0(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > The run-wise functionality was added after selxavg was written as a way to > help debug. If you want all the runs in your group analysis, why not turn > off the run-wise flag? > > On 1/22/2020 4:40 PM, Rami Hamati wrote: > > External Email - Use Caution > > Hello freesurfers, > > I'm attempting to run second-level analysis on separate runs of a brain > scan, that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003, > pr004) as described in selxavg3-sess --help. > > But, when attempting to concatenate the data using isxconcat-sess, (as > described here: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLev… > ) there is no similar -run-wise function. I've searched the list and no > similar errors have been reported.. I am wondering if there is a command or > workaround for this. Thank you very much! > > -- > Rami Hamati, MSc. > Royal's Institute of Mental Health Research > Molecular Imaging Laboratory (MIL) > 1145 Carling Ave, Ottawa, ON K1Z 7K4 > > Rami.Hamati(a)theroyal.ca<mailto:Rami.Hamati@theroyal.ca> > rhama036(a)uottawa.ca<mailto:rhama036@uottawa.ca> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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