Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

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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mri_vol2surf wrong hemisphere
by Defenderfer, Matthew K 07 Dec '17

07 Dec '17

Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public use. I took this volume and applied the mri_vol2surf command to it to create 2 overlays of the parcels, 1 for each hemisphere. The code was: mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh The code ran, but the LH parcels in the volume were transferred to the RH on the surface and vice versa. This is a problem since the parcellation is not symmetric across hemispheres.This is not a problem with the volume either as I looked at it overlayed with the MNI152 brain in fslview and saw that the parcels were on the correct hemisphere. Another problem is that 1 of the frontoparietal parcels, number 24, was not found on the surface of either hemisphere after turning it to a surface. I don't know why this would be the case since there are all cortical parcels. I have also tried this with a volume ROI that is only located on the left hemisphere. After running essentially the same vol2surf command as above, the ROI only appeared on the RH surface. I am using mri_vol2surf from Freesurfer v6.0.0 Any help would be greatly appreciated. Thank you! Best, Matthew Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389

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Re: [Freesurfer] Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors
by Marshall, Anisa 07 Dec '17

07 Dec '17

Dear all, We are seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and brain tumors. Our team includes full-time faculty from Psychiatry, Radiology, Neurosciences, and Radiation Oncology at UC San Diego. This group of researchers and clinical investigators are primarily focused on integrating research imaging tools and genetic information into the clinical work flow to directly and immediately improve patient outcomes. The scholar will work closely with other postdoctoral fellows, medical residents, graduate students, research assistants, and faculty members to help develop methods, analyze structural, diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist with grant applications. The fellow should have strong programming and writing skills, experience in neuroimaging or a related field, and a strong interest in pursuing an academic career path. Applicants with a strong background in bioengineering, cognitive science, and/or experience in machine learning and other multidimensional data integration approaches are encouraged to apply. Location: UCSD Center for Multimodal Imaging and Genetics (CMIG) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: Flexible, but no later than Spring/Summer 2018 This position is located at the UCSD CMIG, which is located on the East Medical Campus in La Jolla, CA in the Altman CTRI. The fellow will share an office with another postdoctoral fellow and have direct access to two 750 GE systems. Please send application to Dr. Carrie McDonald (camcdonald(a)ucsd.edu<mailto:camcdonald@ucsd.edu>). Kind regards, Anisa ---------- Anisa Marshall, MS Neuroimaging Research Associate Center for Multimodal Imaging and Genetics (CMIG) UC San Diego Office phone: (858) 246-0291 a6marshall(a)ucsd.edu<mailto:a6marshall@ucsd.edu>

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Freesurfer December 2017