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30132 discussions

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN
by Mcnorgan, Christopher 08 Dec '17

08 Dec '17

An epiphany lead me to the solution to the problem, which I shall post here since I am apparently due to experience it again in 2019. The NAN values in the GLM matrices were the result of there being a condition that did not appear in any of the .par files across all of the runs. Once these files were edited so that all of conditions 1, 2 and 3 appeared somewhere among these files, selxavg3-sess was able to run. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ <http://ccnlab.buffalo.edu/> * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ > Hi Doug et al., > > It appears I've encountered this problem once before: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647… <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647…> > > Unfortunately there is no record of any resolution (if there was one) in the original thread, and I have no recollection of what the outcome was. Where the thread did leave off was a request for the Xtmp.mat file, so I will include the Xtmp.mat file from the analysis that worked (GoodXtmp.mat) and the one that failed (BadXtmp.mat). > > The error message: > > Creating Design Matrix > ... creation time = 0.019 sec > DoMCFit = 1 > ntptot = 2592, nX = 81, DOF = 2511 > Saving X matrix to /home/chris/SEM/FS_0231/bold/FAM.self.sm4.down.rh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > Error in cond (line 35) > s = svd(A); > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > Curiously, unless something was overlooked, the same analysis was carried out on another dataset that went through the same preprocessing steps without incident. > > The Xn matrix in BadXtmp.mat contains 3 columns of NaN (:,[7,8,9]), but without knowing how those values are calculated, I can't take a principled stab at fixing the problem. > > Thanks for your help, > Chris > > <GoodXtmp.mat><BadXtmp.mat> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail.

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Postdoc opportunity at MEEI
by Bruce Fischl 08 Dec '17

08 Dec '17

Mass Eye and Ear is looking for a computational postdoc: masseyeandear.org/simonyanlab/jobs

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Using Nifti parcellation with Freesurfer
by Ricardo Valle 08 Dec '17

08 Dec '17

Dear Freesurfer community, I would like to be able to use any preexisting Nifti atlas with Freesurfer’s parcellation methods. As a proof-of-concept, I am attempting to use the parcellation scheme produced by Finn and colleagues (2015) with mris_ca_train and mris_ca_label. I have some questions about this. I wonder whether what I am trying to do makes sense. To train mris_ca_train, I would feed it the Collin MNI template space and Finn’s parcellation scheme (which is registered to Collin MNI as far as I can tell). This is not ideal for two reasons. First, it would be better to train mris_ca_train on a group of subjects. Second, the anatomical data and parcellation data come from two separate data sets. Is my understanding correct so far? On the other hand, the other way I can think of to parcellate an individual’s data based on an atlas is to register the data and the atlas and assign labels from the atlas to the individual where they overlap. This doesn’t seem any better to me. Are there other ways of using atlases to parcellate individual data that I am not aware of? Right now, I am stuck trying to produce an annot file to give to mris_ca_train. I ran mri_vol2surf --src shen_1mm_268_parc.mgz --hemi lh --mni152reg --out_type paint --o ./lh-surf-parc.mgz where shen_1mm_268_parc.mgz is the result of converting the parcellation scheme from nifti to mgz with mri_convert. The resulting mgz file seems reasonable. However, I don’t know how to make an annot file from it. Is there a way to do this? I also attempted the following: mris_sample_parc -ct ./ctab.txt -sdir .. -file ./ctab.txt FS lh shen_1mm_268_parc.mgz lh-parc.annot The results don’t make sense to me and I don’t understand how mris_sample_parc works. What is the purpose of the translation file (-file option)? From what I’ve read on the wiki, mris_sample_parc is used to sample a manual parcellation done on an individual subject’s volume to that subject’s surface. In my case, the “subject” (Collin MNI brain) happens to be aligned with the parcellation. Does it make sense to run mris_sample_parc? Thank you. Best regards, Ruy

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selxavg3-sess problem: SVD input matrix contains NaN
by Mcnorgan, Christopher 08 Dec '17

08 Dec '17

Hi Doug et al., It appears I've encountered this problem once before: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647… Unfortunately there is no record of any resolution (if there was one) in the original thread, and I have no recollection of what the outcome was. Where the thread did leave off was a request for the Xtmp.mat file, so I will include the Xtmp.mat file from the analysis that worked (GoodXtmp.mat) and the one that failed (BadXtmp.mat). The error message: Creating Design Matrix ... creation time = 0.019 sec DoMCFit = 1 ntptot = 2592, nX = 81, DOF = 2511 Saving X matrix to /home/chris/SEM/FS_0231/bold/FAM.self.sm4.down.rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); Curiously, unless something was overlooked, the same analysis was carried out on another dataset that went through the same preprocessing steps without incident. The Xn matrix in BadXtmp.mat contains 3 columns of NaN (:,[7,8,9]), but without knowing how those values are calculated, I can't take a principled stab at fixing the problem. Thanks for your help, Chris

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Extracting the Transformation from Cortical Surface to Sphere
by Adam Li 08 Dec '17

08 Dec '17

Hi Freesurfer developers, I am rather new (a few days in fact) to Freesurfer, so forgive me if I have some lack of knowledge. I am currently working with T1 MRI and CT scans of patients that are undergoing epilepsy surgery, and am interested in using the transformation that freesurfer uses to "inflate" the cortical surface into a sphere for "inflating" the electrode contacts onto the spherical surface as well. However, I am not sure if Freesurfer saves this transformation matrix done on the cortical surface? If so, is there a way I can extract that? Thank you! -- Best Regards, Adam Li Graduate Student in Biomedical Engineering Johns Hopkins University & School of Medicine (805) 807-5898 | LinkedIn <http://www.linkedin.com/in/adamli2392> | Personal Website <http://adam2392.pythonanywhere.com/> | ali39(a)jhu.edu

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error in mri_surf2surf FS60
by Duran, Tugce 08 Dec '17

08 Dec '17

Dear FS Experts, I recently got the attached error in mris_preproc and mri_surf2surf in FS 6.0. These commands work in FS 5.3. But somehow FS 60 doesn’t run the files correctly. Any ideas? Thanks, Tugce Duran

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Re: [Freesurfer] new Amygdala and Hippocampus segmentation
by Iglesias Gonzalez, Eugenio 08 Dec '17

08 Dec '17

Hi Erik, You can runsegmentHA_T2.sh on your FS processed subjects. You don’t need to run segmentHA_T1.sh first. The choice is whether you want to use T1+FLAIR (USE_T1=1) or only FLAIR (USE_T1=0). This command will generate outputs for both hippocampus and amygdala. The output will include multiple segmentations at different hierarchies, but only one text file with all the volumes. Regarding your old 6.0 measures: they’re safe because they used the suffix v10, and the new ones use the suffix v20 Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon(a)rcsi.ie> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 8 December 2017 at 14:15 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] new Amygdala and Hippocampus segmentation Hi FS experts, I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run? for example would the following generate the hippocampus and amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ? segmentHA_T2.sh subject001 subject001_Flair.nni.gz T1andFlair USE_T1 /subject001 Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir? Thanks for any help you can provide . Erik Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D37030.F38C36B0] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.ie<http://www.rcsi.ie/> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE

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IndexError: list index out of range
by Ayushi Shukla 08 Dec '17

08 Dec '17

Hello everyone, I am trying to run a cortical thickness analysis in QDEC. I have recon-all and qcache but while trying to run asegstats2table, I keep getting the error-list index out of range. asegstats2table --subjects 101 102 103 INSP104 INSP105 INSP107 INSP108 INSP109 112 113 114-S 115-S 116-S 117-S INSP119 INSP120 INSP121 INSP122 123 INSP124 125 126 INSP-127 INSP-129 INSP130 INSPD131 INSPD132 133 INSPD134 136 INSP137 INSP138 INSP139 INSP140 INSP141 INSP143 INSP144 --meas volume --tablefile Vol_HV_stats.txt SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse seg = strlst[1] # segmentation id is in the 2nd field IndexError: list index out of range. This does not happen when I run the same command for a separate group of subjects. The recon-all and qcache ran without error. So I was hoping you could help me resolve this issue. Warm Regards Ayushi Shukla Research Assistant National Institute of Mental Health and Neurosciences Bangalore, India

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new Amygdala and Hippocampus segmentation
by Erik O'Hanlon 08 Dec '17

08 Dec '17

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[Re] Infant Atlas {Disarmed}
by li ki 07 Dec '17

07 Dec '17

Hi Emma Thanks for your reply~ As I am not major in neuroscience, maybe it is quite hard for me to label the image. But thanks a lot and I will try. Would you please help me: 1. The link you provided mentions a new pipeline for infants. Is it integrated with specific infant .gcs atlas file? I am happy as this is what I really want. 2. I provide a new UNC link here(https://www.nitrc.org/projects/pediatricatlas). Can I use these in FreeSurfer? But I find it hard to replace the default one. Thanks for you time again. Best, Lemon ________________________________ Hi Lemon Please see the mailing list archive here for some guidance (the answer is the same for infants): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56037.html I couldn't see the UNC link you provided. But the basic steps for creating your own atlas are: -label every voxel of the brain in Freeview (for every subject to be used in the atlas) -run mri_ca_train -run rebuild_gca_atlas.csh script in $FREESURFER_HOME/bin Best, Emma --------- Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging ________________________________ From: freesurfer-bounces at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <freesurfer-bounces at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> on behalf of li ki <lizhq94 at outlook.com<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> Sent: Wednesday, December 6, 2017 2:41 AM To: freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Subject: [Freesurfer] Infant Atlas Hi experts, We are presently involved in a project for analyzing MRI data of 1-3 year old children using FreeSurfer. We cannot find a correct infant atlas. From online search, I know that an infant atlas is being developed which will be integrated into FreeSurfer in the future. （link https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ ） Can I know when this will be available? If not soon, is there any other methods for us to generate an infant(kid) atlas? Also I know there are infant atlas from UNC(http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-a…, how can I use this atlas in Freesurfer? Best, Lemon -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20171206/6…

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