Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

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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Version 6.0 patches for hi-res data
by Alexopoulos, Dimitrios 24 Jan '20

24 Jan '20

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.

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Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version
by Rene Seiger 24 Jan '20

24 Jan '20

External Email - Use Caution Dear all, I recently saw that the page of the hippocampal module for FS6 (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) seems to be obsolete and it looks as if this module will be replaced by a newer version in the near future (now dev version, https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) However, I am not entirely sure how those two modules differ in terms of hippocampal subfield segmentation, when the "FS60" parcellation scheme is used in the new module. It is stated that 'it mimics the FreeSurfer 6.0 hippocampal module', but is the output 1:1 comparable? Thank you very much and kind regards, René -- *Dr. René Seiger* Research Associate *Medical University of Vienna* Department of Psychiatry and Psychotherapy Division of General Psychiatry NEUROIMAGING LABS (NIL) - PET, MRI, EEG, TMS & Chemical Lab Waehringer Guertel 18-20, A-1090 Vienna Phone +43 (0) 1 40400-38250 rene.seiger(a)meduniwien.ac.at <mailto:rene.seiger@meduniwien.ac.at>http://www.meduniwien.ac.at/neuroimaging/ <http://www.meduniwien.ac.at/neuroimaging/>

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freesurfer container - freeview error
by Arnaud Boré 24 Jan '20

24 Jan '20

External Email - Use Caution Dear Freesurfer' experts, I've created a singularity container from the official docker hub freesurfer repository (https://hub.docker.com/r/freesurfer/freesurfer) When running: singularity exec freesurfer.sif freeview I get this error: freeview_bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No suche file or directory. I would like to know if this is something related to the containers or the host computer and some tips to fix this. I tested the singularity on different computers/laptops and ended up with the same error so I think there is an issue with the singularity/docker container. Thank you in advance Arnaud

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FreeSurfer analyses in MatLab
by Graduate Imaging 24 Jan '20

24 Jan '20

External Email - Use Caution Hello, I recently ran a vertex wise analysis on two different projects the first had three groups with three co-variates that looked at if group membership was associated with brain volume. The second project had two groups with three co-variates looking at psychiatric x BMI interaction effect on brain volume. I'm interested in running ROI analyses in matlab to ensure the same matrices were used. To run the ROI analyses I'm going to important the design matrix from the vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown below: X = load('Xg.dat'); C = load('C.dat'); y = load('ROI.dat'); text file containing participant ROI values from the DKT atlas. [beta rvar] = fast_glmfit(y,X); [F pvalues] = fast_fratio(beta,X,rvar,C My first question is the beta values that are calculated from fast_glmfit are unstandardized is there anyway way to have it compute standardized values? My second question is when I ran the ROI analyses looking at the diagnosis x BMI interaction effect it outputs an array of beta values for each regressor. In addition to each groups beta value (for BMI) I'm interested in the beta value of the interaction (ie diagnosis x BMI). I was wondering how do i go about obtaining this? Would I have to create a new matrix with the interaction term included in it? If so would the analysis essentially be one group with the diagnosis x BMI interaction term plus the three co-variates?

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Troubleshooting FLAIR Images
by Swanson,Clayton 24 Jan '20

24 Jan '20

External Email - Use Caution Hi FreeSurfer Developers, After looking through the archives my question still remains. I am wondering if the same rules apply for editing/correcting FLAIR images as it does for T1 images. For example, can I add control points to the WM.mgz then re-run recon-all using the command recon-all - s <subject> -autorecon2-cp -autorecon3. For visualization I have attached a screenshot of what I am attempting to correct. Thank you for your help, Clayton [cid:9B76FB99-0BA6-4427-99CE-74076577DE40@hsd1.co.comcast.net.]

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help: fs-fast group level analysis per run
by Rami Hamati 24 Jan '20

24 Jan '20

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 rhama036(a)uottawa.ca

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Freesurfer January 2020