Freesurfer May 2019

freesurfer@nmr.mgh.harvard.edu

95 participants
141 discussions

Conjunction analysis on the results of task-based fMRI
by Zhi Li 07 May '19

07 May '19

External Email - Use Caution Dear Freesurfer experts, I would like to investigate the overlap between two contrasts with conjunction analysis. May I know how should I use mri_glmfit-sim to correct the combined sig.nii.gz of contrast A and contrast B? Another question is if I want to do conjunction analysis on the corrected p maps of both contrasts, which file should I use, 'perm.th30.pos.sig.cluster.nii.gz' or 'perm.th30.neg.sig.voxel.nii.gz'? Besides, what is the difference between the p value in 'perm.th30.pos.sig.cluster.nii.gz' and 'perm.th30.neg.sig.voxel.nii.gz'? I tried to visualize the 'perm.th30.neg.sig.voxel.nii.gz', the figure was a little weird that the significant part in this file seemed to the the boundary of the uncorrected 'sig.nii.gz', is that correct? I asked a similar question before, maybe the post has been lost that I did not get answers. I am still confusing on the forming of the file 'perm.th30.pos.sig.cluster.nii.gz'. If the value in each cluster of this file is CWP, how does this p value generates (the CWP within a cluster is the same, but zero outside clusters)? Any suggestions would be much appreciated. Thanks and best wishes, Lizhi

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dimensions swapped with head first-prone acquisition
by Caspar M. Schwiedrzik 07 May '19

07 May '19

External Email - Use Caution Hi! I have data acquired on a Siemens scanner with head first-prone. When I convert the dicom files to MGZ, left and right and superior and inferior, respectively, are swapped. The anterior-posterior dimension is ok. I am wondering what the correct way to correct this is? Following this entry in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that I can use mri_convert with --in_orientation for that, and the images indeed look correct when I do this. I am however wondering whether I have to do the conversion to COR and fix the RAS coordinates as well? I found a 2007 entry on the mailing list about that https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.h…, but it does not specify how to proceed. Your advice would be appreciated! Thanks, Caspar

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Re: [Freesurfer] recon-all stops in CORRECTING DEFECT
by Marina Fernández 07 May '19

07 May '19

External Email - Use Caution Hi Bruce, Thank you very much for your reply. We try to do it in the way that you told me but we could see (when we loaded [r/l]h.orig.nofix inside the brainmask.mgz and wm.mgz) that in this subject there aren't yellow lines that delimitate the white matter in a lot of slices. On the other hand, we also could see that the posterior defect isn't caused by a bunch of skull/muscle not removed by the stripping. This part is brain but it seems like a defect because the other parts of the brain near this part aren't taken into account in the [r/l]h.inflated.nofix. You can see it in attached files. I also attach this problematic subject. We would be very grateful if you can check this subject and tell us your opinion, because we suspect that we will not solve this problem only with control points and the wm edit tool because there isn't lines in a lot of slices. Thank you in advance! Best wishes, Marina pre_030.zip <https://drive.google.com/file/d/17rQ9F-kUY_oo-CEblNJ916otWk-jy4Pv/view?usp=…>

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Creating mask using mri_label2vol
by Holmes, Emma 07 May '19

07 May '19

External Email - Use Caution Dear list, I'm new to freesurfer and would like to create a volumetric region of interest from the Destrieux atlas labels, to mask my spm12 results. All my images have been normalised so I just need the mask in avg305T1 space. I tried running the following command: mri_label2vol --label ctx-lh-S_intraparietal-and_Parietal_transverse.label --temp [MATLAB_PATH]/spm12/canonical/avg305T1.nii --o [PATH_TO_OUTPUT_DIR]/test.mgz --reg /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz I get the following print-out and error message: $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.50000 -0.00000 -0.00000 45.50000; -0.00000 -0.00000 -0.50000 54.50000; -0.00000 0.50000 -0.00000 45.50000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8 nHits Thresh: 0 Loading registration from /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz regio_read_register(): Success Error reading inplaneres from /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz As I'm new to freesurfer, I'm probably missing something simple. I've tried searching the archives (e.g., I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/018159.ht…) and notice that many use register.dat as the --reg input, and I assume this is where the problem arises here. However, I'm not sure how to go about generating this file, as I'm using the average brain: Do I need to run a full surface reconstruction on the avg305T1.nii file? Or is there a simpler way to get around this? I have mni152.register.dat in my freesurfer directory but no mni305.register.dat equivalent. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux localhost.localdomain 3.10.0-957.10.1.el7.x86_64 #1 SMP Mon Mar 18 15:06:45 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Platform: Windows 8.1, running through VirtualBox 6.0.6 Thanks in advance for your help with this, Emma

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How to get the difference between motion, NU intensity correction images and the originate image?
by chen 06 May '19

06 May '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. According to my results, there exsit difference between ROIs. So, i want to check the difference between the originate image and the images after motion and NU intensity correction to confirm the most variation area. How can i get this information?I am looking forward to your kind suggestions.Best regards,Jiachen ------------------ 首都医科大学宣武医院杜佳晨

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trac-all -bedp error
by Daniel Callow 06 May '19

06 May '19

External Email - Use Caution Hello, When running the pre.job script created from /Volumes/DANIEL/trac-all -bedp -jobs job -c /Volumes/DANIEL/ dmrirc.long.example.sh which I am trying to submit by running setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh foreach subj (AES101 AES102 AES104 AES107 AES108 AES109 AES110 AES111) bedpostx_preproc.sh /Volumes/DANIEL/dti_freesurf/trac/Ex.${subj}.long.base_${subj}/dmri bedpostx_preproc.sh /Volumes/DANIEL/dti_freesurf/trac/Rest.${subj}.long.base_${subj}/dmri end end I get the following error. [255a-280:/Volumes/DANIEL/dti_freesurf] amos% ./pre.job.sh Copying files to bedpost directory usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory /usr/local/fsl/bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected Done Is this the incorrect way of trying to run trac-all -bedp in parallel? And if so how should I go about running the job scripts? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Volume computation from Surface and Thickness
by Daniela Vecchio 06 May '19

06 May '19

External Email - Use Caution Dear all, referring to the lh.aparc.DKTatlas40.stats Freesurfer output, I would like to know how the GrayVol column is computed as just multiplying ThickAvg*SurfArea I obtained different values. Thanks in advance for helping! Dani

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Transforming Amygdala nuclei atlas to MNI space
by Dev vasu 04 May '19

04 May '19

External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then i convert .mgz file to NIFTI using mri_convert Cortico_amygloid.mgz Cortico_amygloid.nii.gz. Later i tried to transform Cortico_amygloid.nii.gz to MNI space using FLIRT but i notice seed region Cortico_amygloid.nii.gz is oriented in different place. Kindly let me know what more i have to do , in order to transform .mgz label into MNI space. Thanks Vasudev

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Petsurfer: Motion Correction
by Shane Schofield 04 May '19

04 May '19

External Email - Use Caution Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Transforming Amygdala nuclei atlas to MNI space
by Dev vasu 03 May '19

03 May '19

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Freesurfer May 2019