Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

freesurfer with infants MRI
by Chiara Bulgarelli 16 Feb '16

16 Feb '16

Dear All, I would like to ask you for some advice about segmenting MRI from infants data. In particular, these are my questions: 1. if I have two different templates related to two different time points in the 1st year of life, and one of this two is clearly a bad quality MRI image (even visible from the T1 image), the other one is quite good. While with the good one I can reconstruct and segment the image perfectly, with the bad one the software is of course missing lots of part during the reconstruction. Is there the possibility to set up some lower threshold in the ‘recon-all' script to allow the segmentation to get more areas considered, even with this bad quality image? 2. I know that the program register the volume with the MNI305 atlas, that is supposed to work well with adults but not with infants: I am actually trying to avoid in my whole neuroimaging analyses (also with other softwares) to “stretch” the infants brain to an adult one. From the high quality MRI infants image that I was able to segmented, the output seems to be fine, but my concern was whether using as a reference an adult brain could affect the results in my case, although the segmentation seems to be well done. I checked the FreeSurfer website but I couldn’t find this information! Any advice would be really appreciated! Best Regards Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01(a)mail.bbk.ac.uk // bulgarelli.chiara3(a)gmail.com

3 3

wm-hypointensities variables
by Otília 14 Feb '16

14 Feb '16

Greetings, I am wondering if there is some information regarding the meaning of "wm-hypointensities" and "non-WM-hypointensities" variables from the aseg.stats file, ie, what features are included in these variables and how FS computes them. I checked previous posts that have the same issue I have now. I find some non-zero, (some cases have "quite big") WM-hypointensities values for healthy young brains. I find it odd. I would appreciate some additional information about these issues. Thank you! Best regards,

2 4

curved Surface projection
by Ashkan Faghiri 13 Feb '16

13 Feb '16

Hello I know it is not the best place to ask this kind of question. But I don't know any place to ask a question like this. I am looking to display "curved Surface projection" for brain mri (like explained in http://www.ajnr.org/content/24/6/1045.full) Can any one suggest me a tool to do this. Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

1 0

Longitudinal analysis--mass univariate
by John Anderson 12 Feb '16

12 Feb '16

4 7

freeSurfer make option is not compatible with pial refinement option
by Antonin Skoch 12 Feb '16

12 Feb '16

Dear FreeSurfer experts, I have some inquiries concerning the "make" option in recon-all: 1. It seems to me that the freeSurfer "make" option in recon-all (at least in 5.3.0 version) is not compatible with -FLAIRpial / -T2pial option. I made some manual edits which required rerun of autorecon2 and autorecon3. The "recon-all -make all" did not rerun pial refinement, which means that the resulting surfaces were generated completely without any pial refinement. Therefore, as I noticed that, I had to rerun recon-all -autorecon3 -FLAIRpial in all affected subjects. Are you aware of this bug/pitfall? I think that this is quite a problem since user need not notice this unexpected behavior which can seriously affect the final results. The user can believe he has surface refined, but instead they are not. I think that modification of recon-all.makefile could solve this problem. 2. I also found that there is no "make" option for local gyrification index. Would you consider also to implement that? 3. My last question is concerning the touch files. It seems that most of the "make" directives do not examine touch files, but the original (volume or surface) files. Therefore, it seems that most of the touch files are never used. What is the significance of touch files? 4. I also noticed some inconsistency in documentation: reconAllTable for 5.3 version does not contain -FLAIRpial / T2 pial step at all. https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3 They are documented only in dev version https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable but it does not correspond to 5.3.2 version - there seems to be difference in the position of -nuintensitycor step in the processing flow. Is there an actual table of reconstruction steps for 5.3.2 version? Regards, Antonin Skoch Institute for Clinical and Experimental Medicine Prague, Czech Republic

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R: R: R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 12 Feb '16

12 Feb '16

Please also look the file attached. This the sig.nii.gz (subcortical, MNI) overlapped on f.nii. ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 12-feb-2016 17.16 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: R: Re: To use a ROI.label as seed in FS-FAST Please also consider that the T1, f.nii and ROI.ii.gz (obtained by label2vol) are nice overlapped. The brain.mni305.2mm.nii seem to be strange (see the image attached). In the sig.nii.gz the cluster are bad coregistered and some of those out are of the brain. Thanks Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 12-feb-2016 0.23 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm). Thanks Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 11-feb-2016 4.48 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way, you might be able to figure it out for yourself rather than have to wait a day or so for us to respond. doug On 2/10/16 4:20 PM, stdp82(a)virgilio.it wrote: If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 8-feb-2016 20.35 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST Thanks. I have down a right ad left ROI on the surface. Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz mri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.config fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh Segmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol? Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

How to convert a surface label to .nii
by stdp82＠virgilio.it 12 Feb '16

12 Feb '16

file attached

1 0

R: R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 12 Feb '16

12 Feb '16

Please also consider that the T1, f.nii and ROI.ii.gz (obtained by label2vol) are nice overlapped. The brain.mni305.2mm.nii seem to be strange (see the image attached). In the sig.nii.gz the cluster are bad coregistered and some of those out are of the brain. Thanks Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 12-feb-2016 0.23 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm). Thanks Stefano ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 11-feb-2016 4.48 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST I may have gotten the exact form of the flag wrong. When it says an option is not known, you should try running the command with --help to see if something similar is there. In this way, you might be able to figure it out for yourself rather than have to wait a day or so for us to respond. doug On 2/10/16 4:20 PM, stdp82(a)virgilio.it wrote: If I use: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon ERROR: Option --fill-ribbon unknown ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 8-feb-2016 20.35 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST Thanks. I have down a right ad left ROI on the surface. Next, I have run: mri_label2vol --label ramgseed_rhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz mri_label2vol --label ramgseed_lhsurf.label --temp $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh --o LEFT_ROI.nii.gz mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg RIGHT_ROI.config fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg LEFT_ROI.config fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config fcseed-sess -s subj1_FS -cfg LEFT_ROI.config but during fcseed-sess this error occurs: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz Loading /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh Segmentation fault ----Messaggio originale---- Da: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Data: 8-feb-2016 4.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST Use mri_label2vol to convert the label into a volume in the anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon if the label is surface-based. When running fcseed-config, specify the volume with the -seg option and use -segid 1 On 2/7/16 3:16 PM, stdp82(a)virgilio.it wrote: Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer. How can I do it? Should I use mri_label2vol? Thanks. Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

abnormal inflated surface
by Jasmin Alves 12 Feb '16

12 Feb '16

Hello freesurfer, I received this odd inflated surface image. I am not sure if this is something that can be fixed via a registration step or should be fixed in another step. Your input as to how to correct this image would be greatly appreciated. Also, I noticed that this participant's hippocampal volume is half the amount compared to the rest of my participants. Is it possible these two problems are related or am I possibly dealing with two separate issues? I have attached a screen shot of both problems. Thank you very much, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

3 3

Freeview to mark only one specific area
by Luis Fernado Silva Castro de Araújo 12 Feb '16

12 Feb '16

Hello Freesurfer experts, I want either a 2D or 3D picture of one of my subjects image, but with only one colored area. For example, I would like to mark the lh_lateralorbitofrontal_area. It seems that the tool to visualize images in Freesurfer is freeview, however I can't find the label for the left hemisphere lateralorbitofrontal_area in the GUI. It is not listed in the Volumes tab with the aparc+aseg item ticked. I did not find information in your website, maybe I missed. Could you please provide a pointer towards the answer? Maybe I missed where it is taught at the documentation, a simple link would do. Thanks, luis

2 1

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