Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

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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Recon editing + FLAIRpial
by Matthieu VANHOUTTE 18 Mar '19

18 Mar '19

External Email - Use Caution Dear Experts, Having launched recon-all process on one subject with supplemental FLAIR data in order to better define pial surface, I still need to follow some recon editing during the QC of this patient. However, when re-launching recon-all to take into account manual editing do I have to precise on more time "-FLAIR FLAIR.nii.gz -FLAIRpial" or will it be implicit? Best regards, Matthieu

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QDEC Longitudinal Analysis: Missing spc option from dropdown menu
by Arsenije Subotic 18 Mar '19

18 Mar '19

External Email - Use Caution Dear Freesurfer experts, I am having issues choosing the spc option for my QDEC two stage longitudinal analysis as it is not there. The spc files are all present in my participants files and the Qdecrc file is in the qdec subdirectory containing the line long.thickness-spc. Is there a way to bypass this problem somehow? Thank you, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Longitudinal QDEC
by AKUDJEDU, THEOPHILUS 18 Mar '19

18 Mar '19

External Email - Use Caution Dear All, I am running a longitudinal (2-time points) group cortical analysis in Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a cross-sectional form, I added a text file containing the lines MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc in the qdec directory to guide qdec to know about the newly created files (e.g. lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking up the new files or not reading the text file named Qdecrc.txt (which has the lines above. Will be glad if you could offer any help. Thanks Theo

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tkregister-sess
by Nasiriavanaki, Zahra 18 Mar '19

18 Mar '19

Dear Freesurfers Hi I was checking the functional on structural data registration quality by using the below command. tkregister-sess -s $subj -fsd bold -per-run -bbr-sum I observed high values (around 0.9) for one of my subjects, and I figured out, that subject was registered to another subject's structural data by mistake. I re-did the recon (in a new folder) and checked the registration again, the values are still the same! However when I check my log files, it seems that the recon is done correctly and the snapshots from QA_tools don't look bad. I appreciate if you could please let me know what you think. Thanks a lot Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Time-series extraction from each vortex in a ROI
by Zhi Li 18 Mar '19

18 Mar '19

External Email - Use Caution Hello Freesurfer experts, I would like to extract time series of pre-processed data from each vortex of ROIs in a annotation file, may I ask how could I achieve this? I tried 'mri_segstats' which only generated the mean time series of each ROI. I also tried Matlab, but 'read_surf' doesn't seem to work in import brain functional data (e.g., fmcpr.up.sm5.fsaverage.lh.nii.gz). If there is a way to import functional data into Matlab? And how could I use the information in the annotation file to get time series of each vortex in a ROI? Thank you very much. Best regards, Lizhi

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Freesurfer March 2019