Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

mri_convert --in_center
by Song, Da-Yea 20 Mar '19

20 Mar '19

External Email - Use Caution Hello, Is it possible to change the origin of the aseg.mgz file? I tried mri_convert --in_center -117 -219 145 aseg.mgz new_aseg.img. When I opened the new_aseg.img file the origin seems to be at 0 -127 0. Any suggestions would be greatly appreciated! Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Error in QDEC analysis between group and individual case
by 김정식 20 Mar '19

20 Mar '19

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Re: [Freesurfer] Omitting aseg regions from segmentation
by zalewk 19 Mar '19

19 Mar '19

External Email - Use Caution Thanks for getting back to me Doug/Bruce. Sounds good, yes I definitely would want to wait until the bugs have been worked out before utilizing latest release. If your dev team needs contributors to document/write the ex-vivo processing stream I'd be happy to step in and help, I've been running various ex-vivo scan acquisitions through freesurfer for a year at this point. I also have experience in C and shell scripting if that helps, as it seems that's what much of freesurfer is written in. Not sure who I would talk to about that. Best, Kody Zalewski Message: 11 Date: Tue, 19 Mar 2019 14:53:30 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Omitting aseg regions from segmentationTo: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <235d9f13-1eda-1d76-920f-d30b9c467635(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" ... but know that the dev version is not fully tested -- there may be significant bugs that will not be uncovered until it is tested. As such, we may not be able to support any problems you run into. ________________________________ On 3/18/19 8:12 PM, Bruce Fischl wrote: Hi Kody there definitely are flags like this in the dev version. e.g.: case "-no-cerebellum": case "-nocerebellum": case "-NO-CEREBELLUM": case "-NOCEREBELLUM": set nocerebellum=( -nocerebellum) breaksw ; Maybe you should just grab the dev version? And sorry, we haven't documented the ex vivo processing stream yet as it is too much of a work-in-progress. cheers Bruce ________________________________ On Thu, 14 Mar 2019, zalewk wrote: External Email - Use Caution Hi Bruce, In response to your previous email, in v6.0 it doesn't look like recon-all has a "-no-cerebellum" flag (or any cerebellum-related flags), I did verify that the recon-all script in the bin folder had hemisphere-specific flags available however. Is there any documentation on this? It still seems as if I'm missing something here, was it maybe included in previous versions of freesurfer and removed? Best, Kody Zalewski Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Omitting aseg regions from segmentation To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1903041505530.3767(a)gate.nmr.mgh.harvard.edu><mailto:alpine.LRH.2.20.1903041505530.3767@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Kody yes, there are some hidden options to recon-all for this. Take a look at the script for things like -no-cerebellum, -rh-only, and see if they are sufficient for what you are trying to do cheers Bruce

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Postdoctoral Position: Neuroimaging of Self-Regulation and Mental Illness
by Jeffrey Spielberg 19 Mar '19

19 Mar '19

External Email - Use Caution Applications are being sought for a postdoctoral fellow with experience in neuroimaging methods, data collection, and analysis in the PD Lab (Personality and Dysregulation Lab) of Dr. Naomi Sadeh at the University of Delaware. The lab is currently conducting studies examining brain networks that contribute to impulsive and harmful behaviors in adults with and without mental illness. The ideal candidate will have a strong background in functional/structural MRI (e.g., FSL, FreeSurfer), programming (e.g., MATLAB), and an interest in impulsivity, self-regulation, and/or externalizing psychopathology (e.g., antisocial personality disorder, alcohol/substance use disorders). Clinical training is not required, but would be considered an asset. The position is open to individuals who have completed a Ph.D. in Psychology or related field or an M.D. Preference will be given to individuals with strong organizational skills, written and oral communication skills, experience working in research teams, and a demonstrated ability to work well with others. Applications from any area of Psychology are encouraged, especially from individuals who have an interest in externalizing disorders. In addition, the fellow will have the opportunity to learn cutting-edge network-analysis methods (e.g., graph theory). The postdoctoral researcher will be heavily involved in data analysis and the preparation of findings for manuscript publication and conference presentations. The anticipated start date is Summer 2019 (with flexibility) and would last for a two-year period with potential for renewal. If you are interested in being considered for the position, please send a current CV, a brief statement of interest that outlines your qualifications for the position, reprints of selected papers, and the names of three professional references to Dr. Naomi Sadeh at nsadeh(a)udel.edu. -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Office: 307 McKinly Laboratory Lab: Suite 405 Wolf Hall Phone: 302.831.7078 Email: jmsp(a)udel.edu Website: http://sites.udel.edu/jmsp/

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Repairing problems with aparc
by Donovan Roediger 19 Mar '19

19 Mar '19

External Email - Use Caution Hello, We have noticed that in about 10-15% of our subjects, the banksSTS is overestimated to include tissue on the gyral surface of the superior temporal gyrus, middle temporal gyrus, or other adjacent parcels. What is the preferred method to fix this problem? I know that we *can* directly edit the offending labels in tksurfer, but is that the general method-of-choice for repairing problematic parcellations in otherwise good looking data? Thanks! Donovan Roediger Dep't of Psychiatry, Univ. of Minnesota

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Insula Parcelation
by Vasile, Eduard 19 Mar '19

19 Mar '19

Dear Freesurfer team, I was wondering if you are aware of an extensive label for insula parcellation (LH and RH), something more advanced then the DK atlas. I've been struggling to find one. Thank you! Kind regards Eduard Vasile On 3/18/19, 12:01 PM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: 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. mris_preproc not running (Sims, Sara A (Campus)) 2. Longitudinal QDEC (AKUDJEDU, THEOPHILUS) 3. Re: mris_preproc not running (Greve, Douglas N.,Ph.D.) 4. Re: Longitudinal QDEC (Greve, Douglas N.,Ph.D.) 5. Re: Cortical thickness values extraction issue (Giuliana Klencklen) 6. Re: Cortical thickness values extraction issue (Greve, Douglas N.,Ph.D.) 7. Re: Cortical thickness values extraction issue (Giuliana Klencklen) 8. skip subjects already processed (Akshay Patel) 9. tkregister-sess (Nasiriavanaki, Zahra) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Mar 2019 15:12:39 +0000 From: "Sims, Sara A (Campus)" <snolin(a)uab.edu> Subject: [Freesurfer] mris_preproc not running To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <24C66DC0-853A-4C52-943B-0AB3E731FA7C(a)uab.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello! I have 786 subjects that I am trying to do a paired difference analysis using mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it on a handful of subjects and it works wonderfully. However, when I run it on all the subjects it outputs an empty file. I think part of my problem is that I am having to do 1572 flags to enter all the subjects files (which I made a script to create, I did not hand type them). Is there a better way to do this? Do I just have too many subjects? This is what I have that isn?t working: mris_preproc --target fsaverage --hemi lh --isp $in/${network}/100206.${run1}/lhsurf.mgh --isp $in/${network}/100206.${run2}/lhsurf.mgh --isp $in/${network}/100307.${run1}/lhsurf.mgh --isp $in/${network}/100307.${run2}/lhsurf.mgh ??. --out $out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f $sublist --paired-diff --no-cortex-only Thanks for the help! Sara Sims

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Clusterwise correction using Permutations
by Victor Montal 19 Mar '19

19 Mar '19

External Email - Use Caution Dear Freesurfer experts, I am very interested in using your permutation approach in order to correct our uncorr analyses using the newly proposed approach (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.…) However, I am facing some problems that I hope you can assist me on. We are computing the uncorrected stats using the mri_glmfit option --frame-mask. However, when I run the (latest) version of mri_glmfit-sim, as in the tutorial, I get the errors: """ INFO: unrecognized mri_glmfit cmd option --frame-mask ... probably not a problem INFO: unrecognized mri_glmfit cmd option ../rh.framemask.mgh ... probably not a problem """ My concern is, since the command is not considering the frame-mask option, it will not also permutate the mask accordingly to the GLM design permutation. Am I wrong or the sim command will permute the mask without problem? I have also tried to run the mri_glmfit with the --sim option. In this case, I don't receive any warning/info, thus, I am assuming it takes into account the permutation of the frame-mask, or it does not? One possible workaround would be to create the cluster-extension csd file by myself, but I would know if there is any solution for this already implemented in Freesurfer. Thank you in advance for your help! Victor M

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One Group analysis
by Jose Pineda 19 Mar '19

19 Mar '19

External Email - Use Caution Dear all, Im currently running a cortical thickness longitudinal analysis on a group of 50 patients. The difference between timepoints is less than 4months, so I do not expect large ageing effect (although there might be some). I would like to test for specific cortical changes after neurosurgery. I have read that it is not possible to run one-sample ttest within qdec, what alternatives do I have then. - Could I just compute the average change in pc1 or rate? - Would it then be advisable to run a paired-ttest analysis between timepoints instead of merging the images using long_mris_slopes? Any advice would be appreciated. Best, José -- José Angel Pineda-Pardo Postdoctoral Researcher hmCINAC - HM Puerta del Sur Av Carlos V 70, Móstoles, Spain

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Omitting aseg regions from segmentation
by zalewk 19 Mar '19

19 Mar '19

External Email - Use Caution Hi Bruce, In response to your previous email, in v6.0 it doesn't look like recon-all has a "-no-cerebellum" flag (or any cerebellum-related flags), I did verify that the recon-all script in the bin folder had hemisphere-specific flags available however. Is there any documentation on this? It still seems as if I'm missing something here, was it maybe included in previous versions of freesurfer and removed? Best, Kody Zalewski Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Omitting aseg regions from segmentation To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1903041505530.3767(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Kody yes, there are some hidden options to recon-all for this. Take a look at the script for things like -no-cerebellum, -rh-only, and see if they are sufficient for what you are trying to do cheers Bruce ________________________________ ________________________________ On Mon, 4 Mar 2019, zalewk wrote: > > ????????External Email - Use Caution???????? > > Hello Freesurfer team, > > I am currently working processing the volumetrics of exvivo brains, many of which do not have a > brainstem/cerebellum. > It seems this often results in a subcortical alignment that isn't optimal, and fails to create the > pial/wm surface where freesurfer attempts to label more ventral non-zero voxels as > brainstem/cerebellum. Currently, I have to manually edit the aseg.auto_noCCseg.label_intensities.mgz > and aseg.presurf.mgz to fix this. > > Is there a way to omit aseg labels (like the brainstem/cerebellum) from the processing stream that > I've overlooked? If not, would there be a potential alternate solution such as creating a second > atlas from the original sans these ROIs and have the cross-sectional stream still run normally? > > Best, > Kody Zalewski

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Using Schaefer 2018 atlas with FreeSurfer
by Fatih SOĞUKPINAR 19 Mar '19

19 Mar '19

External Email - Use Caution Dear FreeSurfer developers *For my MRI data, I have cortical parcellations and segmentations for the Destrieux and Desikan-Killiany atlases. Now, **I am attempting to use Schaefer 2018 atlas (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… <https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc…>) for cortical parcellation together with FreeSurfer. Currently what I have tried is:* *1)* mri_surf2surf --srcsubject fsaverage --trgsubject $SubjectID --hemi lh --sval-annot /ourSchaferAtlasDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order.annot --tval ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot *2) *the same of 1) for the right hemisphere *3) *mri_label2vol --annot ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot --temp ourSubjectDirectory/mri/our T1.nii --o ourSubjectDirectory/mri/sch_lh.mgz --subject $SubjectID --identity --hemi lh * 4) * the same of 3) for the right hemisphere * 5)* mri_concat ourSubjectDirectory/mri/sch_lh.mgz ourSubjectDirectory/mri/sch_rh.mgz --sum --o ourSubjectDirectory/mri/sch_lh+rh.mgz However, at this point, the resulting .mgz file (sch_lh+rh.mgz) is a bit strange : When I open the file in matlab, I see that it's volume field is 218*182*182 , while the same data results in 256*256*256 for Destrieux Atlas. Furthermore, values of the volume field of sch_lh+rh.mgz change between 0-200 , while this is 0-12175 for the Destrieux Atlas. These effects are also apparent in the ultimate results (parcellation.nii images, which I generate by using .mgz files). They are not aligned properly and their intensity is also erroneous. I suspect that we have a mistake in the above pipeline. *My questions are: * * 1) Is there simpler way to do this task? (For example, a simple addition to the recon-all function, etc.)* * 2) If not, what else should I do to be able to get the correct parcellations ? * *PS: I am a bit new to the FreeSurfer and MRI processing, so please accept my apologizes if this is a simple question... * Thank you in advance and best regards.

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