Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

Mri_segstats on longitudinal data (NVoxels)
by Ferdi van de Kamp 10 May '17

10 May '17

Hi all, My question is twofold using an user specified ROI in MNI512-space I ask Freesurfer to create tables for both cross-sectionally& longitudinally processed data. Mri_segstats performed over both cross-sectional data folders and longitudinal data folders However, when inspecting the data, the NVoxels for all time points in the longitudinal data are equal, while in the cross-sectional they differ (and are generally larger). Is this to be expected? In addition to NVoxels and mean intensity, our lab would like to use other measures such as thickness, does anyone know the correct function to call for that information? Right now the pipeline look like this: Step1 standardised labels from volumes This step is focused on the ROIs, not the subjects, is submitted as a single job Uses *mri_vol2vol *and *mri_cor2label*. Step 2 Create personalised labels, volumes & tables This is the part that is submit to the cluster for each subject (separate for cross-sectional and longitudinal). It uses *mri_label2label*, *mri_label2vol *and *mri_segstats*. Thanks! Ferdi van de Kamp

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Question of longitudinal processing
by jahanvi patel 10 May '17

10 May '17

Hello list, I have a simple question about the LongitudinalTwoStageModel tutorials on freesurfer website. It is from this link https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel long_mris_slopes --qdec long.testretest.qdec \ --meas thickness \ --hemi lh \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm 15 \ --qcache fsaverage \ --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ --isec-labels lh.testretest.fsaverage.cortex.label My question is, what is the content of long.testretest.qdec ? I understood till 1st stage was done, we got only one file which is long.qdec.table.dat. Could anyone help to clarify my question? Thanks a lot Jahanvi

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Two group two time longitudinal analysis
by Livia Liu 10 May '17

10 May '17

Dear FS experts， I have two group and two times to do longitudinal cross analysis. I looked your answer in https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45870.html and https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52032.html Sorry, I can’t understand what you said” you can either subtract the two time points and then do a regular group analysis” " subtract tp1 from tp2 manually and pass the result to mri_glmfit." How to subtract the two time manually and how to do then ? Would you please tell me more details? And in my analysis, if I use the paired analysis, how to design paired.fsgd and paired-diff.fsgd? In http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis I am sorry to only see how to do in one group. Looking forward to reply, and thanks very much. Kind regards, Livia

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Color LUT help
by Stephanie Otto 09 May '17

09 May '17

Hello, I am running some DTI analyses and can't seem to find the Color LUT number for the arcuate fasciculus. Is there a number assigned for this ROI or another way to identify it? Thank you, -- Stephanie Otto Graduate Student, Cognitive and Brain Sciences Program Department of Psychology, MSS 414 University of Nevada, Reno sotto(a)nevada.unr.edu

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TRACULA exports white matter tract labels without DTI data
by Yong Li 09 May '17

09 May '17

Dear Anastasia, Dear Bruce, As a newbie in using freesurfer, I would like to ask for help to output white matter tract labels of each subject without DTI data. This topic was briefly discussed last April by Holleran, Laurena ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46459.html) but I don't find how to do it. To be specific, I would like using TRACULA 'to mapping the tracts from the atlas onto the individual subject' as suggested by Bruce in his reply to Laurena. Other questions are: How to view the extracted white matter tract labels in the individual space? freeview or trackvis or other viewers? Could TRACULA deal with DTI data in Nifti format? If not, is there a way to reliably convert DTI data from Nifti to DICOM (*.dcm)? Hope I make myself clear. Thank you very much in advance! Best regards, Yong

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TRACULA tracts corrections
by Joëlle Ismay Rosanne Van Der Molen 09 May '17

09 May '17

Hi Anastasia & Freesurfer experts, I've been going through the different processing steps of the longitudinal TRACULA stream and as some tracts needed to be rerun, I set up my dmrirc file as recommended (subjlist limited to the subject to correct; pathlist limited to the path(s) to rerun; npcts corresponding to the tract to rerun; set reinit = 1) and then ran this file with the -prior flag, followed by the -path flag. However, surprisingly, it looks as if all the tracts are being reconstructed again, not only the one that is specified under pathlist... At least, that is the impression I get when looking at the new merged_avg33_mni_bbr.mgz file, and at the trac-all.log file. This brings me to my 2 questions: 1) Is there a way to check that TRACULA reinitializes and reconstructs only the desired tracts? 2) If indeed all tracts were reinitialized and rerun, how can I fix that? I suspect I'm then doing something wrong in the configuration of the dmrirc file, but I cannot seem to find out what. I added the dmrirc file and the trac-all.log file; I would greatly appreciate it if you could help me out. Additional info: freesurfer version is 6.0, operating system is OS X Yosemite 10.10.5. Let me know if you need any other information or files. Best, Joëlle

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recon-all freezes while CORRECTING DEFECT 60
by Weisholtz, Daniel S.,M.D. 09 May '17

09 May '17

Hello Freesurfer Developers, I am trying to run recon-all -all and the procedure is freezing while trying to correct what appears to be a large defect (vertices=36706). The source T1 image is not great quality due to rippling artifact, but I have inspected brainmask.mgz, wm.mgz, and aseg.mgz and I cannot identify a large defect. The dura was not completely removed, and I tried improving this by using various watershed thresholds as well as using gcut. I also tried manually removing the remaining dura, but none of this was helpful. I also tried using -T2FLAIR, but this did not seem helpful either. I am attaching the recon-all.log. This does not include the edits I made to brainmask.mgz. That was done on a separate attempt. This does include the -T2FLAIR, as you can see in the recon-all.log file. 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: OS X Yosemite 10.10.5 3) recon-all.log attached I very much appreciate any assistance you can provide. Happy to send any of the data if it would be helpful. Sincerely, Dan Weisholtz

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mri_convert : pix vs no pix ?
by Shane Schofield 09 May '17

09 May '17

Dear Doug,I am trying to flip some PET images so that they are in the same orientation as the T1.I came across this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you explain what what it means to change the pixel data? Should I use pix or without pix? For context I am working with PET data (in img/hdr formats) that seemed to have been flipped L/R somehow. Thank you.

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illustration of a nifti volume on fsaverage
by james pardon 09 May '17

09 May '17

Dear All, Apologies in advance for the naive question. Could you please let me know what is the best way of transferring a nifti overlay volume to fsaverage, solely for illustration purposes? I think I should start by registering with fsaverage volume and then overlay with Freeview, but I'm not sure what tools from Freesurfer I should use for 1) between subject volume registration (nifti volume to fsaverage volume) 2) fsaverage volume to fsaverage surface. Thank you, James

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White matter volume of a costumized Gyrus
by Josue Luiz Dalboni Da Rocha 09 May '17

09 May '17

Dear Freesurfer team, I am working with calculated volumes of a gyrus (a costumized label). I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in label format). According to the freesurfer tutorial (as I understood), one of the stats outputted from mris_anatomical_stats is the volume of the gray matter surrounding the white/gray matter border (a surface) specified by the inputted label. We are actually interested in the white matter volume (instead of gray matter volume) inside this ROI (a gyrus in our case) specified by the label. I didn't find yet a command in freesurfer from where I can extract the white matter volume of a gyrus from a costumized label. Could someone advise me? Best regards, Josue

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Freesurfer May 2017