Freesurfer

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30080 discussions

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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skip subjects already processed
by Akshay Patel 18 Mar '19

18 Mar '19

External Email - Use Caution Hello, I have a subset of subjects that were processed with an older version of FreeSurfer and would like to run FreeSurfer in the subjects directory such that it skips all the subjects already processed by my version of freesurfer and only reruns recon-all ... for those aforementioned subjects. When I do this, will the file structure and files for the subject be overwritten? How does FreeSurfer behave in this case? How does it behave for subjects directories that have already been successfully processed with the same command (including options) attempting to process it at the moment? Would appreciate any help thanks. Best, Akshay

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Cortical thickness values extraction issue
by Giuliana Klencklen 18 Mar '19

18 Mar '19

External Email - Use Caution Hi FS experts, I did group-level, surface-based, vertex-wise analysis for baseline and longitudinal data. I used Qdec and do the same work with the fsgd version (mri_glmfit-sim command) to double-check the data. I created label files with tksurfer for each of the clusters showing a significant between-group difference. Then, I used the following command stream to extract the cortical thickness values for each subject and cluster: mri_label2label, mris_anatomical_stats, and aparcstats2table. E.g., mri_label2label --srcsubject fsaverage --srclabel /home/jagust/gklenck/Long_MRI/lh.ac-baseline-rostralmiddlefrontal.label --trgsubject ${s}_tp1 --trglabel ${s}_tp1/label/lh.ac-baseline-rostralmiddlefrontal.label --hemi lh --regmethod surface mris_anatomical_stats -l lh.ac-baseline-rostralmiddlefrontal.label -t lh.thickness -b -f ${s}_tp1/stats/lh.ac-baseline-rostralmiddlefrontal.stats ${s}_tp1 lh aparcstats2table --subjects ${s}_tp1 --hemi lh --parc ac-baseline-rostralmiddlefrontal --meas thickness --tablefile ${out_dir}/lh.ac-baseline-rostralmiddlefrontal.aparc_stats.txt Subsequently, when I conducted between-group comparisons for each cluster, a couple of clusters (7 out of 16) do not show a significant difference - which does not make sense. This problem seems to appear randomly. Help to the FS archives, I tried to use mri_segstats command but was not able to find a correct combination of arguments. If this is the right track to solve this problem, what combination of arguments should I use? And if this is not, do you have any idea how I can solve this problem? Many thanks in advance. Regards, Giuliana -- Giuliana Klencklen, Ph.D. Helen Wills Neuroscience Institute University of California, Berkeley 118 Barker Hall Berkeley, CA 94720-3190 510-395-0040 giuliana.klencklen(a)berkeley.edu

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回复：回复： Error with mri_label2label(Segmentation fault(coredumped))
by 310913949 18 Mar '19

18 Mar '19

External Email - Use Caution Dear experts, I think I need to send you the information of my ROI,i am not sure whether it is something wrong. This is the part of the 4gt.label I drew.And the attachment is the picture of the 4gt.label. Thanks again. #!ascii label , from subject vox2ras=scanner 59455 -1 43.255 58.553 -24.301 0.0000000000 -1 43.255 58.553 -24.301 0.0000000000 -1 42.058 58.629 -24.306 0.0000000000 -1 40.860 58.704 -24.310 0.0000000000 -1 40.860 58.704 -24.310 0.0000000000 -1 40.799 57.729 -24.310 0.0000000000 -1 40.799 57.729 -24.310 0.0000000000 -1 39.601 57.805 -24.314 0.0000000000 -1 39.601 57.805 -24.314 0.0000000000 -1 38.404 57.880 -24.318 0.0000000000 -1 38.404 57.880 -24.318 0.0000000000 -1 37.206 57.955 -24.322 0.0000000000 -1 37.206 57.955 -24.322 0.0000000000 -1 35.947 57.056 -24.326 0.0000000000 -1 35.947 57.056 -24.326 0.0000000000 -1 34.749 57.131 -24.330 0.0000000000 -1 34.749 57.131 -24.330 0.0000000000 -1 33.552 57.207 -24.334 0.0000000000 -1 33.552 57.207 -24.334 0.0000000000 -1 32.293 56.307 -24.338 0.0000000000 -1 32.293 56.307 -24.338 0.0000000000 -1 32.293 56.307 -24.338 0.0000000000 -1 32.232 55.333 -24.338 0.0000000000 -1 32.232 55.333 -24.338 0.0000000000 -1 31.034 55.408 -24.342 0.0000000000 -1 29.836 55.483 -24.346 0.0000000000 -1 29.836 55.483 -24.346 0.0000000000 -1 29.836 55.483 -24.346 0.0000000000 -1 28.639 55.558 -24.350 0.0000000000 -1 28.639 55.558 -24.350 0.0000000000 -1 28.577 54.584 -24.350 0.0000000000 -1 27.318 53.685 -24.354 0.0000000000 -1 27.318 53.685 -24.354 0.0000000000 -1 27.257 52.710 -24.354 0.0000000000 -1 27.257 52.710 -24.354 0.0000000000 -1 27.257 52.710 -24.354 0.0000000000 -1 27.196 51.735 -24.354 0.0000000000 -1 27.196 51.735 -24.354 0.0000000000 -1 27.135 50.761 -24.354 0.0000000000 -1 27.135 50.761 -24.354 0.0000000000 ------------------ 原始邮件 ------------------ 发件人: "邓刊"<310913949(a)qq.com>; 发送时间: 2019年3月14日(星期四) 上午10:03 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: [Freesurfer] 回复： Error with mri_label2label(Segmentation fault(coredumped)) External Email - Use Caution Sure.This is the full terminal output: root@zourushi-All-Series:/usr/local/freesurfer/subjects/PT1_4# mri_label2label --srclabel label/4gt.label --s PT1_4 --trglabel 4gtreg.label --hemi rh --paint 30 pial --trgsurf pial Could not set locale No such file or directory Could not set locale srclabel = label/4gt.label srcsubject = PT1_4 trgsubject = PT1_4 trglabel = 4gtreg.label regmethod = surface srchemi = rh trghemi = rh trgsurface = pial srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 1 PaintMax 30.000000 SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 59455 points in source label. Starting surface-based mapping Reading source registration /usr/local/freesurfer/subjects/PT1_4/surf/rh.sphere.reg 59455 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... /usr/local/freesurfer/bin/mri_label2label: line 3: 4446 Segmentation fault (core dumped) mri_label2label.bin "$@" ------------------ 原始邮件 ------------------ 发件人: "Greve, Douglas N.,Ph.D."<DGREVE(a)mgh.harvard.edu>; 发送时间: 2019年3月13日(星期三) 凌晨0:06 收件人: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] Error with mri_label2label(Segmentation fault(coredumped)) Can you send the full terminal output? On 3/12/19 10:36 AM, 310913949 wrote: External Email - Use Caution Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the command line: mri_label2label --srclabel 4gt.label --s PT1_4 --trglabel 4reg.on-pial.label --hemi rh --paint 30 pial --trgsurf pial. But it reported error: Line 3:4445 Segmentation fault(core dumped), mri_label2label.bin "$@". Can you tell me how to solve this problem?Is it wrong to use the mri_label2label? Thanks. Best wishes， Kan Deng _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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