Freesurfer

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30132 discussions

Trying to get functional scan working
by Brad Matushewski 11 May '17

11 May '17

Hello Freesurfer crowd. I am working on try to get my first fMRI scan working. I have come a long ways in terms of setting things up but have reached a road block that I have unable to get past. I have been following along the slides from the power point presentation "FSFAST Part 2". I got as far as slide #32: Preprocessing Command". Specifically, I entered the following command: preproc-sess -sf sessids -surface fsaverage lhrh -mni305 -fwhm 5 -pre-run Things started to happen but finished rather quickly. I looked through the text output and it would appear that it cannot find the bet.fsl tools(?). I looked at the directory to where it was looking at it IS in there (i.e. /usr/local/freesurfer/bin/bet.fsl) I also labelled things exactly as outlined: (i.e. /usr/local/freesurfer/subjects/handedness/project/Sess01) I have attached a couple text files from the output logs. What can I try next? [Logo] Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447

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mri_label2label with close operation
by Hengda He 11 May '17

11 May '17

Hi Freesurfer Developers, I'm trying to map the vertices of caudal middle frontal in one subject into the space of another subject by using mri_label2label. And I used the method mentioned in this https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2015-November/042298.… We are using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I noticed the mri_label2label in v5.1 has the bug of getting holes in the mapped labels( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42600.html) So I am using the /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin from freesurfer-x86_64-unknown-linux-gnu-dev5-20160513. For example, we have source Labels(aparc-lh-003_5thCol.label), which are all in SurfaceRAS coordinates: #!ascii label , from subject FreeSurfer vox2ras=TkReg 8 104996 -35.679 16.281 25.156 1 104997 -36.480 16.439 25.362 2 104998 -37.443 16.702 25.369 3 105705 -41.554 16.840 28.930 4 105716 -40.445 17.153 28.046 5 105720 -39.570 17.200 26.959 6 131017 -29.315 12.915 45.422 7 131030 -31.304 12.514 46.455 8 By running this: /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh We got mapped Labels(aparc-lh-003_5thCol_Reg2MNI.label), which are all in SurfaceRAS coordinates: 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000 But the mapped labels I got from the mri_label2label in v5.1 and that from using mri_label2label.bin in dev are quite similar to each other when applying the method to around 3500 labels. So I am wondering if the bug of getting holes was fixed by providing morphological operations in the updated mri_label2label like close operation. If it is true, I am confused about the mapped labels from mri_label2label with close operation. For example, with the same source labels above, I ran /usr/local/freesurfer/freesurfer_dev/bin/mri_label2label.bin --srclabel aparc-lh-003_5thCol.label --srcsubject FreeSurfer --trglabel aparc-lh-003_5thCol_Reg2MNI_close2.label --trgsubject FreeSurferMNI152 --regmethod surface --hemi lh --close 2 And we got mapped Labels(aparc-lh-003_5thCol_Reg2MNI_close2.label): 119096 -39.670 37.222 12.833 3.0000000000 117433 -44.642 35.253 14.575 4.0000000000 118250 -43.206 35.844 14.273 5.0000000000 119091 -42.114 36.692 14.044 6.0000000000 120517 -26.436 38.614 21.780 7.0000000000 121236 -25.959 39.757 24.739 8.0000000000 1321 -22.346 -82.436 -9.530 0.0000000000 121253 -26.213 39.504 23.711 8.0000000000 1045 -1.690 -91.572 -40.145 0.0000000000 118251 -18.413 75.394 63.061 0.0000000000 118258 -21.026 75.715 61.847 0.0000000000 119092 -19.797 75.786 62.165 0.0000000000 The problem is that four additional labels 1045, 118251, 118258 and 119092 are not actually on the white matter surface but seem to be right on a sphere(ex. label 1045, 1.690^2+91.572^2+40.145^2=100^2). But I checked all other mapped labels like 119096, they are on the WM surface in the SurfaceRAS coordinates. I am using CentOS release 6.9. Thanks! All the Best, Hengda

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Can I use specific template for FS computing
by shi yao wang 11 May '17

11 May '17

Dear FS experts: We generated a specific population of brain template. Just wondering if FS can use these templates to measure brain volume. thanks Lawrence Emory

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mean hemispheric value in a .mgh
by Damien MARIE 11 May '17

11 May '17

Hi, I’ve a .mgh that is a volume projected on the surface of the same subject at mid-thickness (output of mri_vol2surf) . I would like to extract the mean hemipheric value in this X.mgh. I guess it is possible with mris_anatomical stats but probably my command line is incorrect (see below). Any advices? Thank you and best, Damien mris_anatomical_stats ct_pp1_N4_bet_MP2RAGEcorr -a ct_pp1_N4_bet_MP2RAGEcorr/label/lh.aparc.annot lh R1.mgh computing statistics for each annotation in ct_pp1_N4_bet_MP2RAGEcorr/label/lh.aparc.annot. reading volume /home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/mri/wm.mgz... reading input surface /home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/surf/lh.R1.mgh... ERROR: MRISread: file '/home/damien/bin/freesurfer6/subjects/ct_pp1_N4_bet_MP2RAGEcorr/surf/lh.R1.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!

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Re: [Freesurfer] Freesurfer Digest, Vol 159, Issue 12
by Weisholtz, Daniel S.,M.D. 11 May '17

11 May '17

Dear Bruce, Thank you so much for your suggestions. Unfortunately, I was not able to open lh.defect_labels in freeview. When I try, Freeview crashes. There are no rh surfaces in the surf folder, so I presume this means the problem occurred in the left hemisphere. I was able to view the inflated.nofix and orig.nofix but I’m still not exactly sure what the problem is, and I would be grateful if you could take a look at the subject folder. I will upload it to the ftp site. It is called s117. Thank you! Best, Dan On May 10, 2017, at 10:43 AM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Message: 9 Date: Tue, 9 May 2017 15:54:12 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1705091553090.16219(a)door.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1705091553090.16219@door.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="iso-8859-15" Hi Daniel you can load the ?h.defect_labels as an overlay on either the inflated.nofix or orig.nofix surface and use it to find the location of that defect. Usually this means something big is wrong - it should be obvious looking at the inflated.nofix I would think. If you can't find it, upload the subject to our ftp site and I'll take a look Bruce On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote: 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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Volume comparison between groups and QDEC
by John Anderson 11 May '17

11 May '17

Dear Dr Doug, I have two groups of subjects (80 patients and 40 controls). I analyzed the data using Freesurfer v6.0. I want to study the difference between the groups in "precentral gyrus volume". After "recon-all" I built Qdec table and I used Qdec to compute the comparison by including eTIV a covariate. After correcting the results using Monte Carlo simulation or adjusting for FDR I found no difference between the groups in volume neither in surface area. I adjusted the precentral gyrus volume values for eTIV using the commands: mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2017 mri_label_volume -eTIV $SUBJECTS_DIR/${i}/mri/transforms/talairach.xfm 1948 $SUBJECTS_DIR/${i}/mri/wmparc.mgz 2024 I extracted the adjusted volume values to SPSS then I ran box plots comparison between the groups and I found difference at (P<0.0001) Why Qdec doesn't show the difference between the groups although the p value is very small. What I am doing wrong in Qdec? Is it wrong to include eTIV a covariate? Thank you for any advice John

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hippocampal subfields: which are previous step result (files) needed for the process?
by Guido Pascariello 11 May '17

11 May '17

Hi Experts, I am running Freesurfer v6.0 on a Cluster. I've traied this command: *recon-all -i $IMAGEN -s $SUJETO -all -hippocampal-subfields-T1 -brainstem-structures* Although all step in recon-all works fine, hippocampal-subfields process allocate much more RAM than previous step (10 GB of RAM more or less, and take about 30 mins to be completed, according to other post in the forum). I am thinking in run these one after another, in order to not need to reserve a lot of memory for a long period of time (just for optimization) *I want to know which are the files (from recon-all process) that hippocampal-subfields process needs?* Just to be sure that these will be transferred to the node before the process starts. If you please help me Cheers -- *Bioing. Guido Pascariello* Becario Doctoral CIFASIS - CONICET Grupo de Procesamiento de Señales Multimediales http://www.cifasis-conicet.gov.ar/ Tel/Fax: 54 341 482 6300/ 1771/ 72 Int. 386

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Interpreting PALM-FreeSurfer results
by Sahil Bajaj 10 May '17

10 May '17

Hello FreeSurfer experts, I used PALM toolbox to identify significant clusters after multiple comparison correction using following command: palm -i lh.WASI_LGI.5.mgh -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh -d Xg_WASI_LGI.csv -t Contrast_WASI.csv -m WASI_S5/lh.WASI_LGI.glmdir/mask.mgh -o WASI_S5/ResultsLH_WASI_LGI -C 1.95 -twotail -n 10000 -nouncorrected My output ResultsLH_WASI_LGI_clustere_tstat_fwep.mgz gives me attached screen shot cluster when I open with FreeView. However, I noticed that the colorbar shows values around 0.7 at the red cluster and value 1 elsewhere i.e. values lie between 0 and 1 for the whole brain. (1). From the command and according to previous posts on FreeSurfer forum, I am assuming that significant clusters should be showing value of 1.3 (-logp, where p = 0.05) so I am not sure why the whole brain has value of 1 which is higher than at the red cluster. (2). If significant cluster should show value of 1.3 then isn't it true that the rest of the brain should show values much lower than 1.3 but in actual rest of the brain is showing values higher than 0.7. After displaying partial correlation maps (pcc.mgh), I made sure that the red cluster really has higher correlation than the rest of the brain. I would really appreciate any help if someone could correct me if I am interpreting the results incorrectly? Thanks.

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Obtaining surface normal vector from plial surfaceRAS coordinate
by Jerry Jeyachandra 10 May '17

10 May '17

Hi list, I'd like to extract the surface normal at a location specified in surfaceRAS coordinates after performing segmentation. I know there are methods to extract all vertices and faces then compute face normals from there, but I'm not familiar with methods to relate these to specified coordinates. Thanks Jerry Jeyachandra

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neither NIfTI-1 qform or sform are valid
by shi yao wang 10 May '17

10 May '17

Dear FS experts: There are some error message when I running recon-all as following: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented Are there any problem in raw data? I am using MRICRON to convert DICOM to nii thanks Lawrence

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