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Problems with mri_nu_correct.mni
by Emmanuelle Renauld 06 Nov '15

06 Nov '15

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stat/math tools for MGH file
by Yang, Daniel 06 Nov '15

06 Nov '15

Dear FreeSurfer experts, I have a number of *.cluster.mgh files and I would like to calculate their difference and peak coordinate etc like in fslmaths or fslstats in FSL. For example, given two images, I want to know the brain regions in image1 but not in image2. Could you please recommend the general command line tools I can use for these purposes? Many thanks, Daniel

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Cortical thickness in the depth of a sulcus vs on top of a gyrus: Comparison
by Wrobel, Pawel 06 Nov '15

06 Nov '15

Dear FreeSurfer Developers, I have been wondering, if it is possible to compare cortical thickness in the depth of a sulcus with the the cortical thickness on top of the gyrus? I found the curvature maps in subjects' folders but I don't know how to proceed. I would be very thankful for every hint that You could give me. Thank You for Your assistance! Kind regards, Pawel

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Re: [Freesurfer] the matrix
by Douglas Greve 05 Nov '15

05 Nov '15

make sure there are no blank lines On 11/5/15 6:29 PM, Erik Lindberg wrote: > OK, however I tried several options. With the matrix 1 1 1 1 -1 -1 -1 > -1 0 (using the doss option for age) I basically get the same results > > > Reshaping mriglm->mask... > search space = 74612.446501 > MatrixReadTxT: could not scan value [2][1] > > ERROR: loading C AAA.mtx > olof@olof-Latitude-E5430-non-vPro:/media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec$ > > > /Erik > > > On Thu, Nov 5, 2015 at 11:45 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > The contents of the AAA.mtx matrix are > > {1 1 1 1 -1 -1 -1 -1}/4 0 > > It has to be a simple matrix with simple numbers, no characters, > no math symbols. It will not do the math for you. > > > > On 11/05/2015 05:12 PM, Erik Lindberg wrote: > > Dear Doug, > attached is the folder I tried to run with the matrix. I also > put the .fsgd and the mtx file in the folder as well. > > most grateful for advice on this > > thanks! > > best Erik Lindberg > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > >

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interaction in glm
by Erik Lindberg 05 Nov '15

05 Nov '15

Dear Freesurfer experts, I know this has been an ongoing topic in the mailing list – however I would like to raise the issue one more time. In the choice between doss and dods – I usually check if there is a significant interaction and if so my choice is dods. As I understand it you do not recommend to use doss if an interaction is present. Is the reason for this that I would “over-correct” for the variable in one group while “under-correcting” for the same variable in the other group? It is some time tempting to present result both from a dods and a doss – to tell where the interaction is present, and where difference are present while controlling for the variable But if I understand Doug´s previous comments on this – this would not be a correct approach? Thanks Erik

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Re: [Freesurfer] the matrix
by Douglas N Greve 05 Nov '15

05 Nov '15

The contents of the AAA.mtx matrix are {1 1 1 1 -1 -1 -1 -1}/4 0 It has to be a simple matrix with simple numbers, no characters, no math symbols. It will not do the math for you. On 11/05/2015 05:12 PM, Erik Lindberg wrote: > Dear Doug, > attached is the folder I tried to run with the matrix. I also put the > .fsgd and the mtx file in the folder as well. > > most grateful for advice on this > > thanks! > > best Erik Lindberg -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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R: Re: R: Re: error MRS voxel as seed in FS-FAST
by stdp82＠virgilio.it 05 Nov '15

05 Nov '15

Please see the file attached.Thanks Stefanofile ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 5-nov-2015 15.43 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-FAST sorry, should have been fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& tee doug.log On 11/4/15 6:05 PM, stdp82(a)virgilio.it wrote: Hi Dough, in summary: I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the MRS_MASK.mgz and run: fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean - cfg MRS_MASK.config fcseed-sess -s Control22_FS -cfg MRS_MASK.config ...Writing to /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.fcseed- sess.12305/avgwf.mgh Segmentation fault Therefore, according with your suggestion, I have now run: fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log ERROR: cound not find session -cfg The doug.log is attached. Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 4-nov-2015 16.58 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST First, when running fcseed-config, don't give it the full path, just the path relative to subject/mri (in this case only MRS_MASK.mgz) However, I don't think that is the problem. Please run fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log and send me doug.log On 11/04/2015 04:14 AM, stdp82(a)virgilio.it wrote: Hi list, this error is still occurring: mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz - fsd rest -mean -cfg MRS_MASK.config fcseed-sess -s -cfg MRS_MASK.config During fcseed-sess -s subj -cfg MRS_MASK.config 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/sub/rest/001/tmp. fcseed-sess.97908/avgwf.mgh Segmentation fault I have read your previous message and you can check the MRS voxel features. MRS voxel mask is in subj directory where I have run recon all - all. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ The features are same of other subject that runs fine. data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.010747 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ Thank you very much. Stefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 16-ott-2015 23.15 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] R: Re: R: import FS-FAST results in FSL I'd like to open with FSLview the sig.nii.gz which is produced by selxavg3-sess. If I use mri_surf2vol, which is the template to added in -- template? It should be in Tailairach space? Where can I find the template that I should added? Thanks, Stefano subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz data_type FLOAT32 dim1 27307 dim2 1 dim3 6 dim4 1 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1100.000000 cal_max 49.1815 cal_min -12.3855 file_type NIFTI-1+ Thanks, Stefano ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 29-set-2015 22.09 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL Do you mean surface-based analysis? You'd have to put them back into the volume using mri_surf2vol, write them out as nifti and then run fslview on them On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: Hi list, I would like to import FS-FAST results (conjunction maps) in FSL, opening them by fslview. Could you provide me any suggestion? Thank you very much Best regards, Stefano _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ _______________________________________________ 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

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aparcstats2table
by Yang, Daniel 05 Nov '15

05 Nov '15

Dear FreeSurfer Experts, When I perform aparcstats2table —meas area, does it get it pial.area or white area? I believe it is the pial.area, but this is not documented. If yes, what can I obtain white area via aparcstats2table? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

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Recon-all with lower resolution T2 / Proton Density reconstructions and higher res T1
by Ajay Kurani 05 Nov '15

05 Nov '15

Hello Freesurfer experts, I am working with a database of pre-collected scans. Although the T1 images are collected at 1x1x1 mm^3 resolution, the T2 and proton density scans are .938x.938x3 mm^3. 1) I wanted to see if you think that using the T2 scans for recon-all would hurt or help the pial reconstruction/cortical thickness measurements based on it being much thicker of a volume? 2) Would the scans help with hippocampal subfield analysis based on this resolution? 3) I am interested in using T1/T2 scans for B1 bias field correction (similar to the HCP minimum pipeline paper). I think that using these scans would be ok since the bias field is supposed to be smooth, however I wanted to see your thoughts regarding using the T2 scans of this resolution for the B1 bias-field estimation. Any guidance to any of these questions would be much appreciated! Sincerely, Ajay Kurani

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Trackvis/ DTK Tracula question
by Alan Francis 05 Nov '15

05 Nov '15

Hi Anastasia: I processed 42 brains on Tracula and it ran without problems. I am now trying to run them individually on DTK to test another hypothesis. [I am using the DTK for the first time]. I loaded the diffusion weighted image, filled the parameters in the GUI and ran one single brain. However, it gave me an error which is as follows: ************ 11/5/15 2:07 PM ************ Steps to do: 1. dti_recon "/Users/afrancis/Desktop/Connectome/101309/Diffusion/data.nii.gz" "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti" -gm "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/matrices/gradient.txt" -b 1000 -b0 1 -p 3 -sn 1 -ot nii 2. dti_tracker "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti" "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" -at 35 -m "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_dwi.nii" -it nii 3. spline_filter "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" 1 "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti.trk" 4. trackvis "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti.trk" --------- Launching dti_recon ----------------- Volume dimension: 145 174 145 Voxel size: 1.250 1.250 1.250 Number of b0's: 1 Number of gradient directions: 6 Reading raw data... 100% Reconstructing... 100% b0 threshold used to mask background: 951.79 26709 Writing output... ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_b0.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_dwi.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_fa.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_adc.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_fa_color.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_exp.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_tensor.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_e1.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_e2.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_e3.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_v1.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_v2.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_v3.nii' Process aborted due to error. Thanks so much, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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