[Freesurfer] hippocampal subfields: from posterior to binary masks
Dear list members, as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages) that operates by summing up all the greyscale values https://github.com/neurodebian/freesurfer/blob/master/GEMS/kvlQuantifyPosteriorProbabilityImages.cxx#L107 (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map. What procedure do you use or suggest? I think there are two possibilities here. 1) As written in the paper from Van Leeput et al. http://www.ncbi.nlm.nih.gov/pubmed/19405131, I can *assign each voxel to the label with the highest posterior probability*. Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones. 2) Threshold the subfields such that the volumes of the thresholded mask will equal those calculated by integrating the histogram on the domain 0-255; Formally, find *t* such that: where *H* is the histogram of the subfield. I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling. What do you think about? Luigi. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] seed-based functional connectivity: mkcontrast-sess
When doing a FC analysis, there is no need to run mkcontrast. selxavg3-sess figures out that you are doing a FC analysis and creates the appropriate contrast. The name of the contrast automatically created will be the name of the FC passed to fcseed-config, eg, if you used -fcname L_Posteriorcingulate.dat then, the contrast would be called L_Posteriorcingulate, which can then be passed to other commands (eg, isxconcat-sess) doug On 8/27/14 5:12 PM, Robby De Pauw wrote: Dear FreeSurfer community, I was wondering what my contrast-matrix should look like when doing a first-level analyses since there is no task involved. I tried looking at the -help flag, but I can't see any options for setting a matrix without entering the numb of conditions. This was the command I tried to use: mkcontrast-sess -rmprestim -analysis restingstate.sm05.lh -contrast restingstate.lh I'm sure I'm missing something here, but I can't figure out what to do. Thanks for the already given support!! Best regards, Robby Robby De Pauw, dra. *Ghent University* Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be mailto:robby.dep...@ugent.be ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Cortical gray matter surface area
The WhiteSurfaceArea is the area of the cortical surface defined as the boundary between the WM and the GM. Is this what you want? On 8/27/14 6:56 PM, will brown wrote: Sorry, my mistake. I did mean surface area rather than volume. I am unsure as to how to find the total surface area of the cortical gray matter as ?.aparc.stats file only report WhiteSurfArea. Thanks, Will Message: 17 Date: Wed, 27 Aug 2014 00:48:29 -0400 From: Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical gray matter surface area To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Message-ID: 53fd631d.4070...@nmr.mgh.harvard.edu mailto:53fd631d.4070...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=iso-8859-1 The volume for each structure is given as the 4th column. If you want total GM volume, look in aseg.stats doug On 8/26/14 8:43 PM, will brown wrote: Hi all, I am a little unclear as to how to find the cortical grey matter volume in the stats output files. The ?.aparc.stats file shows: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 What about grey? Thanks, Will ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Difference between surfcluster and volcluster
volcluster is only used for volume-based (ie, 3D) analysis, eg, an fMRI analysis of subcortical structures. surfcluster is used for surfaces doug On 8/28/14 4:33 AM, Katharina Zech wrote: Dear all, I run the surfcluster analysis (mri_surfcluster). But the tutorial tells me that there exists also mri_volcluster: Using the outputs from the estimation step and the simulations, mri_surfcluster (or *mri_volcluster*) will create two outputs: the summary file with a table of the clusters it found, and an output surface map of the clusters wth the cluster-wise p-value. The sample mri_surfcluster command is: mri_surfcluster --src lh.gender_age.glmdir/age/sig.mgh \ --csd lh.gender_age.glmdir/csd1-age.csd \ --csd lh.gender_age.glmdir/csd2-age.csd \ --sum lh.gender_age.glmdir/age/sig.cluster.sum \ --ocp lh.gender_age.glmdir/age/sig.cluster.mgh Could you please tell me the difference betweensurfcluster and volcluster? How do I have to change the preprocessing steps mris_preproc, smoothing (surf2surf), mdi_glmfit and the simulation to get volcluster instead of surfcluster? Thanks in advance! Katharina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Manual editing compared to non-manual editing.
Not that I know of. I've done some of this type of analysis. I've found few effects on group analysis of erasing and cloning but there are effects of putting control points. Of course, it is hard to say how general these results are. doug On 8/28/14 6:54 AM, Kasper Jessen wrote: Hi, Thank you for a good freesurfer course in Copenhagen. After the course i have been wondering if there is available litterature regarding manuel editing versus non-manuel editing? Has any studies investigated the outcome/results from manual editing versus non-manuel editing on the same sample of subjects? Best regards, Kasper Jessen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Qdec question
If you know the vertex you want to extract, then you can run something like mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf out.dat where y.mgh is the stack created by qdec and out.dat is the data file you want doug On 8/28/14 8:37 AM, Abrishamchi, Aurash David wrote: Hello, I still cannot solve this issue. All help will be appreciated. I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the find clusters and go to max button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I can put it in excel and calculate some correlations however I cannot find a way to do so without hovering or clicking on each data point and manually entering the values into excel. As you can imagine this is very tedious when there are 100 subjects and 12 regions that we are looking at. Please let me know if there is an alternative way to export the data into excel or even to a word processing file so that the values can be copied and pasted into excel. Best, Aurash Abrishamchi Research Co Op - NCRI - Massachusetts General Hospital 165 Cambridge Street, Suite 600 Boston, MA 02214 P: 617-726-4284 aabrisham...@mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] selxavg3-sess error
It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001 does that file exist? Have you run preproc-sess? doug On 8/28/14 9:49 AM, Francesca Strappini wrote: Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh -- selxavg3-sess logfile is /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log -- --- /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 Thu Aug 28 16:33:53 IDT 2014 anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output No window system found. Java option 'MWT' ignored. Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. M A T L A B (R) Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopy sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# SUBJ01 ### /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy Extension format = nii.gz ERROR: cannot determine format of /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 ERROR: attempting to read /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 -- ERROR: fast_selxavg3() failed\n ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] mri_preproc
Sorry, 7th order, not 12th doug On 8/29/14 11:51 AM, Douglas Greve wrote: It is based on the 12th order icosahedral surface from which the surface atlas is constructed (fsaverage). doug On 8/29/14 4:06 PM, shinj...@andrew.cmu.edu wrote: Hello, I was still wondering about vertex selection after spherical registration. Once the brains are registered to the same spherical coordinate system, how are the vertices chosen? I noticed that each individual brain initially has a different number of vertices, but in the mri_preproc output file, all the brains have the same number of vertices. How are the vertices chosen? Thanks, Jen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] selxavg3-sess error
Thank you, now it works! Best Francesca 2014-09-08 15:24 GMT+03:00 Douglas Greve gr...@nmr.mgh.harvard.edu: It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001 does that file exist? Have you run preproc-sess? doug On 8/28/14 9:49 AM, Francesca Strappini wrote: Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh -- selxavg3-sess logfile is /usr/local/freesurfer/fsfast/MeytalRetinotopy/log/selxavg3-sess-bold-rtopy.DM.lh-140828163352.log -- --- /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 Thu Aug 28 16:33:53 IDT 2014 anadir = /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/rtopy.DM.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output No window system found. Java option 'MWT' ignored. Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. M A T L A B (R) Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopy sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.DM.lh -s SUBJ01 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m #@# SUBJ01 ### /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/fsfast/MeytalRetinotopy/MRIread.m - outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopy Extension format = nii.gz ERROR: cannot determine format of /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 ERROR: attempting to read /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001/fmcsm5 -- ERROR: fast_selxavg3() failed\n ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help extracting Brodmann areas masks
Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the conversion to native space should be fine). 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of brain anatomy is very limited, but if I understand correctly, this equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, V4 and V5), right? 2- I managed to convert V1, V2 and MT labels to 3d masks using mri_label2vol and it seems to work at first glance when I looked at the generated file with freeView. However, I read in the mailing list that mri_label2vol produces patchy volumes and that it is preferable to use mri_aparc2aseg instead. That's what I can't figure out. From what I understand, mri_aparc2aseg aims to map the surface labels of interest to the segmented volumes? I tried doing the following (I altered some file names/paths for readability): # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot)) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label ---l lh.label --ctab BA.ctab --a annot mris_label2annot --s subject --h rh --l rh.V1.label --l rhV2.label ---l rh.label --ctab BA.ctab --a annot # convert to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o lh.asegTest.mgz When I look at the asegTest.mgz file in freeView, I only see segmented cortical volumes and I can't see anything related to V1, V2 or MT, so I assume that I don't use mri_aparc2aseg correctly, but I can't manage to make it work. Any help would be appreciated! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Intraindividual Correlation
Use mri_glmfit with the --pvr option. You would use one of the modes as the input (--y) and one of the modes as the per-voxel regressor (--pvr). When you make a contrast, you need to include elements for each PVR (the PVR forms a vertex-specific regressor in the design matrix) doug On 8/31/14 5:42 AM, Martin Scherr wrote: Dear Freesurfer-community, here is a question from a Freesurfer newbie. I am trying to correlate vertex measures of function (z) and structure (cortical thickness) vertex wise in the individual subject space of one patient. What would be a good tool for this? Best, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] GLM: table with uncorrected clusters
Run mri_glmfit-sim with --cwp 1 This sets the clusterwise threshold to 1, meaning to keep all clusters regardless of their p-values doug On 9/1/14 9:40 AM, Robby De Pauw wrote: Dear FS-community Thx to Doug I was able to successfully run a first analysis. However, I'd like to have a table of the uncorrected clusters. Is there any flag I can add to write these clusters to some sort of txt-file with the p-values etc.? I'm using the mri_glmfit command. Thanks, Best regards Robby Robby De Pauw, dra. *Ghent University* Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be mailto:robby.dep...@ugent.be ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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] Process with a 0.23T scan
Dears experts, I would be very grateful if help me with the following doubts: 1- My data was collected with a 0.23T scan. How i can process it?,Should i make any kind of pre-process before to begin with recon-all? 2- I want only to get the statistics of the caudate nucleus. Is there any way to obtain only this in the segmentation and therefore save time? Thank you. Dr. Merlin Vedecia -- Nunca digas nunca, di mejor: gracias, permiso, disculpe. Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Process with a 0.23T scan
Hi Merlin hmmm, I 've never seen data from such a low field scanner. Have you tried running it through recon-all? I would worry that it is quite noisy. Try it and see how it goes. And no, there is no way to only get caudate - you need to run at least through the end of autorecon2 to get the complete aseg. cheers Bruce On Mon, 8 Sep 2014, merlinva2...@grannet.grm.sld.cu wrote: Dears experts, I would be very grateful if help me with the following doubts: 1- My data was collected with a 0.23T scan. How i can process it?,Should i make any kind of pre-process before to begin with recon-all? 2- I want only to get the statistics of the caudate nucleus. Is there any way to obtain only this in the segmentation and therefore save time? Thank you. Dr. Merlin Vedecia -- Nunca digas nunca, di mejor: gracias, permiso, disculpe. Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas Infomed: http://www.sld.cu/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] hippocampal subfields: from posterior to binary masks
Dear all, I just found that the equivalence Volume/integral isn't quite correct. The equivalence must be between the volume and something like an expected value of the histogram V = E[H] = ∫xH(x)*dx* (where x is the greyscale value). So, the point 2) described in my previous email becomes (with some intermediate passages) Find the threshold value *thr* such that: Does this make any sense to you? Luigi. 2014-09-08 9:49 GMT+02:00 Luigi Antelmi luigi.ante...@gmail.com: Dear list members, as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages) that operates by summing up all the greyscale values https://github.com/neurodebian/freesurfer/blob/master/GEMS/kvlQuantifyPosteriorProbabilityImages.cxx#L107 (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map. What procedure do you use or suggest? I think there are two possibilities here. 1) As written in the paper from Van Leeput et al. http://www.ncbi.nlm.nih.gov/pubmed/19405131, I can *assign each voxel to the label with the highest posterior probability*. Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones. 2) Threshold the subfields such that the volumes of the thresholded mask will equal those calculated by integrating the histogram on the domain 0-255; Formally, find *t* such that: where *H* is the histogram of the subfield. I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling. What do you think about? Luigi. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] hippocampal subfields: from posterior to binary masks
Dear Luigi, the MAP solution (which maximizes the posterior probability of the segmentation given the image and the atlas) is to assign to each voxel the label with the highest posterior probability. The expected value of the volume of a structure is indeed the integral of the its posterior across the image - which can be very different from the volume stemming from counting the voxels in the discrete MAP segmentation. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Luigi Antelmi luigi.ante...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Cc: Jorge Jovicich jorge.jovic...@unitn.it, Moira Marizzoni mmarizz...@fatebenefratelli.it Sent: Monday, September 8, 2014 3:57:38 PM Subject: Re: [Freesurfer] hippocampal subfields: from posterior to binary masks Dear all, I just found that the equivalence Volume/integral isn't quite correct. The equivalence must be between the volume and something like an expected value of the histogram V = E[H] = ∫xH(x) dx (where x is the greyscale value). So, the point 2) described in my previous email becomes (with some intermediate passages) Find the threshold value thr such that: Does this make any sense to you? Luigi. 2014-09-08 9:49 GMT+02:00 Luigi Antelmi luigi.ante...@gmail.com : Dear list members, as you know, the hippocampal subfields given back by FreeSurfer (posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior probability maps in the range [0-255] (i.e. [0-1] with 8 bit of quantization). Although there is a way to calculate the volume ( kvlQuantifyPosteriorProbabilityImages ) that operates by summing up all the greyscale values (an equivalent method is to integrate the histogram over the range 0-255), to my knowledge there is no freesurfer's routine able to extract a binary mask out of the posterior probability map. What procedure do you use or suggest? I think there are two possibilities here. 1) As written in the paper from Van Leeput et al. , I can assign each voxel to the label with the highest posterior probability . Althought I'm wondering why such a thing, documented in the paper, has not been implemented yet, I do not think this is the right way to do it because this procedure do not make any distinction between low probability voxels and high prob ones. 2) Threshold the subfields such that the volumes of the thresholded mask will equal those calculated by integrating the histogram on the domain 0-255; Formally, find t such that: where H is the histogram of the subfield. I prefer the second option because here low prob values are discarded, and because one can apply the equation to a rigid transformed subfield, thus limiting the partial volume effect of the resampling. What do you think about? Luigi. ___ Freesurfer mailing list Freesurfer@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@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.
Re: [Freesurfer] Freesurfer at 7T
Hi Lucy Jon Polimeni (ccd) probably has the most experience processing 7T data. Jon: can you comment? thanks Bruce On Sun, 7 Sep 2014, Lucy Hiscox wrote: Dear Freesurfer experts, I am currently trying to segment a 7T image at 0.8 isotropic resolution. I have an MPRAGE scan and a Gradient echo, and want to coregister the data before processing to correct for inhomogenities, but unsure whether I can use FSL instead of SPM. I am following these instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I am new to SP8 and not sure what I would have to do with this information specifically: (i1./i2 .* (i220)) .* 100. Also, is it possible to just use the recon-all process or would you recommend going through each step individually outlined above? Is the second option the option for keeping the voxels at 0.8? Furthermore, I read somewhere that you have to use the -cm -aseg command to keep the voxels the same. is this true? Best wishes and many thanks, Lucy ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] help extracting Brodmann areas masks
p.s. probably you should use the ?h.BA.thresh.annot, which is the annot containing the labels thresholded to have the correct area cheers Bruce On Mon, 8 Sep 2014, Bruce Fischl wrote: Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the conversion to native space should be fine). 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of brain anatomy is very limited, but if I understand correctly, this equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, V4 and V5), right? 2- I managed to convert V1, V2 and MT labels to 3d masks using mri_label2vol and it seems to work at first glance when I looked at the generated file with freeView. However, I read in the mailing list that mri_label2vol produces patchy volumes and that it is preferable to use mri_aparc2aseg instead. That's what I can't figure out. From what I understand, mri_aparc2aseg aims to map the surface labels of interest to the segmented volumes? I tried doing the following (I altered some file names/paths for readability): # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot)) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label ---l lh.label --ctab BA.ctab --a annot mris_label2annot --s subject --h rh --l rh.V1.label --l rhV2.label ---l rh.label --ctab BA.ctab --a annot # convert to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o lh.asegTest.mgz When I look at the asegTest.mgz file in freeView, I only see segmented cortical volumes and I can't see anything related to V1, V2 or MT, so I assume that I don't use mri_aparc2aseg correctly, but I can't manage to make it work. Any help would be appreciated! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Functional connectivity
You need to load it as an overlay onto a surface. If you mapped your FC onto the native subject space, then use the subject's surface. If you used fsaverage, then use the fsaverage surface. doug On 09/03/2014 11:58 AM, Martin Scherr wrote: Dear Freesurfer experts, We are trying to perform a resting state functional connectivity analysis (seed based, seed = PCC) in a single patient. How can we visualize the map of the (expected) DMN of this single patient in freeview? We tried an overlay with subjectname/mri/orig.mgz and session/bold/fc.lpccseed.surf.lh/pr001/L_Posteriorcingulate/sig.nii.gz which didn't work. Please help! Best, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
That was an oversight. I've attached a version that should work. Can you
test it for me? Once I know it works I'll check it in to tree.
doug
On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
Dear FS experts,
I have a question about a MC output file. When I run the MC sim
(using mri_glmfit-sim) on the surface, it generates a bunch of files
including a 'sig.masked.mgh', which is nice for displaying the
significance map limited to the clusters that survive the MC
correction. However, when I run it on the volume, it doesn't generate
this specific file. Does anyone know the reason for that? Is there an
alternative way to display the significance map that show only the
clusters that survive the MC correction?
Many thanks!
Hamdi
--
Hamdi Eryilmaz, PhD
Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email:heryil...@partners.org mailto:heryil...@partners.org
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/
#!/bin/tcsh -f
set VERSION = '$Id: mri_glmfit-sim,v 1.36.2.6 2013/06/05 17:06:31 greve Exp $';
set inputargs = ($argv);
set glmdir = ()
set nulltype = ();
set nsim = ()
set thresh = ()
set csdbase = ()
set simsign = ()
set cwpvalthresh = .05
set Overwrite = 0;
set DoSim = 1;
set LF = ();
set AllDoneFile = ();
set Seed = ();
set fwhmOverride = ();
set UseUniformPDF = 0;
set UniformPDFMin = ();
set UniformPDFMax = ();
set DiagCluster = 0;
set PBNodeType = ();
set UseCache = 0;
set PermForce = 0;
set UseGRF = 0;
set volsubject = fsaverage;
set subjectOverride = ();
set Bonferroni = 0;
set ReportCentroid = 0;
set annot = aparc
set nJobs = 1;
set DoBackground = 0;
set DoPBSubmit = 0;
set DoPoll = 0;
set tSleepSec = 10;
set CacheDir = $FREESURFER_HOME/average/mult-comp-cor
set CacheLabel = cortex;
set tmpdir = ();
set CleanUp = 1;
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e --help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
set n = `echo $argv | grep -e --version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
if(! -e $glmdir) then
echo ERROR: cannot find $glmdir
exit 1;
endif
set glmfitlog = $glmdir/mri_glmfit.log
if(! -e $glmfitlog) then
echo ERROR: cannot find $glmfitlog
exit 1;
endif
set mask = `stem2fname $glmdir/mask`
if($status) then
echo $mask
exit 1;
endif
if($nulltype != perm) then
set fwhmfile = $glmdir/fwhm.dat
if(! -e $fwhmfile) then
echo ERROR: cannot find $fwhm
exit 1;
endif
# This may be overridden
set fwhm = `cat $fwhmfile`;
else
set fwhm = 0;
endif
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == cwd) print $2}'`
if(! -e $glmfitcwd) then
echo ERROR: cannot find $glmfitcwd
exit 1;
endif
set anattype = volume;
set subject = ();
set hemi = ();
set surf = white;
set y = ();
set wls = ();
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == cwd) print $2}'`
# Go through the original mri_glmfit command-line
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == cmdline) print $0}'`
set glmfitcmd = ($glmfitcmd0);
echo $glmfitcmd
set gd2mtx = dods
set label = ();
while($#glmfitcmd)
set flag = $glmfitcmd[1]; shift glmfitcmd;
#echo $flag
switch($flag)
case --surf
case --surface
set subject = $glmfitcmd[1]; shift glmfitcmd;
set hemi= $glmfitcmd[1]; shift glmfitcmd;
set anattype = surface;
if($#glmfitcmd != 0) then
set c = `echo $glmfitcmd[1] | cut -c 1-2`;
if($c != --) then
set surf = $glmfitcmd[1]; shift glmfitcmd;
endif
endif
breaksw
case --fsgd
shift glmfitcmd;
if($#glmfitcmd 0) then
if($glmfitcmd[1] == doss) set gd2mtx = doss
endif
breaksw
case --label
set label = $glmfitcmd[1]; shift glmfitcmd;
breaksw
case --perm-force
# Probably never gets here
set PermForce = 1;
breaksw
case --y
set y = $glmfitcwd/$glmfitcmd[1]; shift glmfitcmd;
if(! -e $y) then
set y = $glmdir/`basename $y`
if(! -e $y) then
echo ERROR: cannot find $y
exit 1;
endif
endif
breaksw
case --wls
set wls = $glmfitcwd/$glmfitcmd[1]; shift glmfitcmd;
if(! -e $wls) then
set wls = $glmdir/`basename $wls`
if(! -e $wls) then
echo ERROR: cannot find $wls
exit 1;
endif
endif
breaksw
# Ignore these options that have no args
case cmdline
Re: [Freesurfer] Question about mri_convert
Is that all it says? There is no error msg? That is all it prints to the terminal? It should not matter, but try it without the quotes. On 09/03/2014 01:23 PM, Nooshin Zadeh wrote: Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file. *mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] help extracting Brodmann areas masks
Hi Bruce, First of all, thanks for the reply! There was a typo in my initial question, so I rewrote it to make it clearer : # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label --l lh.label --ctab BA.ctab --a myAnnot mris_label2annot --s subject --h rh --l rh.V1.label --l rh.V2.label --l rh.label --ctab BA.ctab --a myAnnot # convert ?h.myAnnot.annot files to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o mySeg.mgz I had not noticed the ?h.BA.annot and ?h.BA.thresh.annot files so I was trying to create an annotation with the labels I was interested in (V1, V2, MT). Maybe I misunderstood what an annotation is, but I thought it was just a collection of labels. I'm not sure what the difference is between .thresh and not .thresh labels. Anyway, whether I run the code above or just the following : # convert ?h.BA.annot to volume mri_aparc2aseg --s subject --annot BA --o BAseg.mgz when I open the .mgz file in freeview, something is obviously wrong (see https://www.dropbox.com/s/evthp4sx40azost/BAseg.png?dl=0 and https://www.dropbox.com/s/s5s7wcwywlaq68o/mySeg.png?dl=0). In comparison, when I convert either the ?h.myAnnot.annot or ?h.BA.annot files using mri_label2vol, it seems fine (see https://www.dropbox.com/s/avo1ot8bitbaeeo/BAlabels.png?dl=0). regards, David On 14-09-08 10:37 AM, Bruce Fischl wrote: p.s. probably you should use the ?h.BA.thresh.annot, which is the annot containing the labels thresholded to have the correct area cheers Bruce On Mon, 8 Sep 2014, Bruce Fischl wrote: Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the conversion to native space should be fine). 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of brain anatomy is very limited, but if I understand correctly, this equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, V4 and V5), right? 2- I managed to convert V1, V2 and MT labels to 3d masks using mri_label2vol and it seems to work at first glance when I looked at the generated file with freeView. However, I read in the mailing list that mri_label2vol produces patchy volumes and that it is preferable to use mri_aparc2aseg instead. That's what I can't figure out. From what I understand, mri_aparc2aseg aims to map the surface labels of interest to the segmented volumes? I tried doing the following (I altered some file names/paths for readability): # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot)) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label ---l lh.label --ctab BA.ctab --a annot mris_label2annot --s subject --h rh --l rh.V1.label --l rhV2.label ---l rh.label --ctab BA.ctab --a annot # convert to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o lh.asegTest.mgz When I look at the asegTest.mgz file in freeView, I only see segmented cortical volumes and I can't see anything related to V1, V2 or MT, so I assume that I don't use mri_aparc2aseg correctly, but I can't manage to make it work. Any help would be appreciated! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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@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
Re: [Freesurfer] help extracting Brodmann areas masks
Hi David - On the difference between .thresh and not .thresh labels: The BA labels come from averaging histologically derived labels from a set of post mortem brains. The non-thresholded version is just the sum of the corresponding labels from the different brains in fsaverage space. So vertices are included even if only one of the brains had their BA in that vertex, which means that these labels are going to be rather large. In the thresholded version, a threshold has been applied to the average BA label, to make it have an area as close as possible to the average area of the individual BA labels. I hope this makes sense. a.y On Mon, 8 Sep 2014, David Provencher wrote: Hi Bruce, First of all, thanks for the reply! There was a typo in my initial question, so I rewrote it to make it clearer : # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label --l lh.label --ct ab BA.ctab --a myAnnot mris_label2annot --s subject --h rh --l rh.V1.label --l rh.V2.label --l rh.label --ct ab BA.ctab --a myAnnot # convert ?h.myAnnot.annot files to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o mySeg.mgz I had not noticed the ?h.BA.annot and ?h.BA.thresh.annot files so I was trying to create an annotation with the labels I was interested in (V1, V2, MT). Maybe I misunderstood what an annotation is, but I thought it was just a collection of labels. I'm not sure what the difference is between .thresh and not .thresh labels. Anyway, whether I run the code above or just the following : # convert ?h.BA.annot to volume mri_aparc2aseg --s subject --annot BA --o BAseg.mgz when I open the .mgz file in freeview, something is obviously wrong (see https://www.dropbox.com/s/evthp4sx40azost/BAseg.png?dl=0 and https://www.dropbox.com/s/s5s7wcwywlaq68o/mySeg.png?dl=0). In comparison, when I convert either the ?h.myAnnot.annot or ?h.BA.annot files using mri_label2vol, it seems fine (see https://www.dropbox.com/s/avo1ot8bitbaeeo/BAlabels.png?dl=0). regards, David On 14-09-08 10:37 AM, Bruce Fischl wrote: p.s. probably you should use the ?h.BA.thresh.annot, which is the annot containing the labels thresholded to have the correct area cheers Bruce On Mon, 8 Sep 2014, Bruce Fischl wrote: Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the conversion to native space should be fine). 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of brain anatomy is very limited, but if I understand correctly, this equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, V4 and V5), right? 2- I managed to convert V1, V2 and MT labels to 3d masks using mri_label2vol and it seems to work at first glance when I looked at the generated file with freeView. However, I read in the mailing list that mri_label2vol produces patchy volumes and that it is preferable to use mri_aparc2aseg instead. That's what I can't figure out. From what I understand, mri_aparc2aseg aims to map the surface labels of interest to the segmented volumes? I tried doing the following (I altered some file names/paths for readability): # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot)) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label ---l lh.label --ctab BA.ctab --a annot mris_label2annot --s subject --h rh --l rh.V1.label --l rhV2.label ---l rh.label --ctab BA.ctab --a annot # convert to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o lh.asegTest.mgz When I look at the asegTest.mgz file in freeView, I only see segmented cortical volumes and I can't see anything related to V1, V2 or MT, so I assume that I don't use mri_aparc2aseg correctly, but I can't manage to make it work. Any help would be appreciated! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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
Re: [Freesurfer] does Tracula correct for CSF contamination
Hi Laura - Apologies, I just found your email and realized I hadn't answered earlier. Which tract are you concerned about being contaminated by CSF? a.y On Wed, 27 Aug 2014, Laura Christine Anderson wrote: Dear Tracula users, does anyone know whether or not Tracula uses any corrections for CSF contamination? Thanks for your time, Laura -- Laura Anderson, B.A. Graduate Student Clinical / Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112 ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Tracula reconstructed tracts quality
Hi Peggy - It's hard to diagnose the problem by seeing only the tracts and not the rest of the data, but this does look very strange. 1.5T is not a problem, but anisotropic resolution is not optimal for tractography, as it can bias the amount of diffusion measured in the direction that the voxels are larger. If you upload the entire data set (all the tracula directories: dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a closer look. https://gate.nmr.mgh.harvard.edu/filedrop2/ a.y On Mon, 8 Sep 2014, Peggy Skelly wrote: Hello Tracula experts, I was wondering if you could comment on the quality of the tracts reconstructed with our 1.5T data. These 2 files are from the same subject at 2 timepoints, processed in the longitudinal stream. Is much of the non-smooth look of the tracts due to the resolution of the dwi scans (1.8x1.8x4mm)? What could be the source of the diagonal lines/gaps in the tracts seen in tp1 when viewed from above? Thanks, Peggy ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] help extracting Brodmann areas masks
Thanks for the reply Anastasia, that makes it more clear. I realized that I was confused due to my inexperience with freesurfer and was using the wrong approach. I did not realize I could simply use the segmented volumes in aseg.mgz corresponding to the visual cortex using http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation as a guideline. thanks, David On 14-09-08 12:39 PM, Anastasia Yendiki wrote: Hi David - On the difference between .thresh and not .thresh labels: The BA labels come from averaging histologically derived labels from a set of post mortem brains. The non-thresholded version is just the sum of the corresponding labels from the different brains in fsaverage space. So vertices are included even if only one of the brains had their BA in that vertex, which means that these labels are going to be rather large. In the thresholded version, a threshold has been applied to the average BA label, to make it have an area as close as possible to the average area of the individual BA labels. I hope this makes sense. a.y On Mon, 8 Sep 2014, David Provencher wrote: Hi Bruce, First of all, thanks for the reply! There was a typo in my initial question, so I rewrote it to make it clearer : # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label --l lh.label --ct ab BA.ctab --a myAnnot mris_label2annot --s subject --h rh --l rh.V1.label --l rh.V2.label --l rh.label --ct ab BA.ctab --a myAnnot # convert ?h.myAnnot.annot files to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o mySeg.mgz I had not noticed the ?h.BA.annot and ?h.BA.thresh.annot files so I was trying to create an annotation with the labels I was interested in (V1, V2, MT). Maybe I misunderstood what an annotation is, but I thought it was just a collection of labels. I'm not sure what the difference is between .thresh and not .thresh labels. Anyway, whether I run the code above or just the following : # convert ?h.BA.annot to volume mri_aparc2aseg --s subject --annot BA --o BAseg.mgz when I open the .mgz file in freeview, something is obviously wrong (see https://www.dropbox.com/s/evthp4sx40azost/BAseg.png?dl=0 and https://www.dropbox.com/s/s5s7wcwywlaq68o/mySeg.png?dl=0). In comparison, when I convert either the ?h.myAnnot.annot or ?h.BA.annot files using mri_label2vol, it seems fine (see https://www.dropbox.com/s/avo1ot8bitbaeeo/BAlabels.png?dl=0). regards, David On 14-09-08 10:37 AM, Bruce Fischl wrote: p.s. probably you should use the ?h.BA.thresh.annot, which is the annot containing the labels thresholded to have the correct area cheers Bruce On Mon, 8 Sep 2014, Bruce Fischl wrote: Hi David what is the annot you are using in mris_label2annot? is it the ?h.BA.annot? cheers Bruce On Mon, 8 Sep 2014, David Provencher wrote: Hi, I am new to freesurfer and I am trying to figure our how to extract 3d masks in native space for the visual cortex (BA 17,18,19) of individual subjects. I have looked at other threads similar to this, but there are still a few things I can't figure out in generating the masks (the conversion to native space should be fine). 1- I ran recon-all and I have V1, V2 and MT labels. My knowledge of brain anatomy is very limited, but if I understand correctly, this equates to BA 17, 18 and V5, so I don't have access to all of B19 (V3, V4 and V5), right? 2- I managed to convert V1, V2 and MT labels to 3d masks using mri_label2vol and it seems to work at first glance when I looked at the generated file with freeView. However, I read in the mailing list that mri_label2vol produces patchy volumes and that it is preferable to use mri_aparc2aseg instead. That's what I can't figure out. From what I understand, mri_aparc2aseg aims to map the surface labels of interest to the segmented volumes? I tried doing the following (I altered some file names/paths for readability): # convert labels to annotation (outputs lh.myAnnot.annot rh.myAnnot.annot)) mris_label2annot --s subject --h lh --l lh.V1.label --l lh.V2.label ---l lh.label --ctab BA.ctab --a annot mris_label2annot --s subject --h rh --l rh.V1.label --l rhV2.label ---l rh.label --ctab BA.ctab --a annot # convert to volume mri_aparc2aseg --s subject --annot myAnnot.annot --o lh.asegTest.mgz When I look at the asegTest.mgz file in freeView, I only see segmented cortical volumes and I can't see anything related to V1, V2 or MT, so I assume that I don't use mri_aparc2aseg correctly, but I can't manage to make it work. Any help would be appreciated! David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Tracula reconstructed tracts quality
Hi Peggy - I looked at the data. Unfortunately, the voxel size is 0.9x0.9x4 in the first time point and 0.9x0.9x5.2 in the second. So not only is the resolution extremely anisotropic, which is problematic for tractography, but it's also different between scans, which almost guarantees that you will find longitudinal changes (except you won't know if it's because the brain is changing or the scan is changing). Finally, the 12 directions that you have may not be sufficient to fit a crossing-fiber model like the ball-and-stick model, which may explain the noisy output. a.y On Mon, 8 Sep 2014, Peggy Skelly wrote: Hello Tracula experts, I was wondering if you could comment on the quality of the tracts reconstructed with our 1.5T data. These 2 files are from the same subject at 2 timepoints, processed in the longitudinal stream. Is much of the non-smooth look of the tracts due to the resolution of the dwi scans (1.8x1.8x4mm)? What could be the source of the diagonal lines/gaps in the tracts seen in tp1 when viewed from above? Thanks, Peggy ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] From bedpostX and recon-all to tracula
Hello Freesurfer Community! Thank you Anastasia and Christopher, I am still getting ending with errors and the log file gives no clue that I have been able to detect, see attached. Any help would be appreciated! On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Kate - There is an example configuration file for tracula in your freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same file is also here: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc If you attach your configuration file and the log file (scripts/trac-all.log), we can try to troubleshoot. a.y On Wed, 3 Sep 2014, Katherine Damme wrote: Hello Freesurfer Community! I have sucessfully completed diffusion preprocessing in FSL and the recon-all of the structural image and would like to use tracula for the tract reconstruction. I keep having trouble with my configuration file. Does anyone have a bedpostX tracula config file they could share as an example?H Thank you! Kate ___ Freesurfer mailing list Freesurfer@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. trac-all.error Description: Binary data dmrirc.local Description: Binary data ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Brodmann Area stats to table
Do you know where can I get the BA28a and BA28b ROIs? 【小孔成像】http://www.conxz.net From: Douglas N Greve Date: 2014-08-08 00:22 To: freesurfer Subject: Re: [Freesurfer] Brodmann Area stats to table There should already be ?h.BA.stats and ?h.BA.thresh.stats. Do those work? On 08/07/2014 09:45 AM, Silas wrote: Hi guys! Is there an easy way to get Brodmann Area stats to table like there is for aseg and aparc stats? Thanks! Silas PS. I looked the question up and it was answered in 2011 - I was just wondering if you guys made an easy way around the problem since then :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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@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.
Re: [Freesurfer] Cortical gray matter surface area
Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary. Will On Wed, Sep 3, 2014 at 1:12 AM, _andre...@sapo.pt wrote: Hi Will, I use the following commands to get surface area from the pial surface: In the subject label dir: mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh. *aparc.pial*.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh. *aparc.pial*.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial Then run aparcstats2table using *aparc.pial* instead of aparc (only because I called this new parcellation aparc.pial) To get the total surface area of each hemisphere I use: In the subject stats dir: mris_anatomical_stats -l ../label/lh.cortex.label -f lh.*total_pial*.stats -b SUBJ lh pial mris_anatomical_stats -l ../label/rh.cortex.label -f rh.*total_pial*.stats -b SUBJ rh pial Then run aparcstats2table using *total_pial* instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like) Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir. I use FS 5.0. Is this what you want? Best, Andreia Citando will brown willbrown1...@gmail.com: Hi all, I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info. ?.aparc.stats reports: Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2 How about the gray matter? Thanks, Will ___ Freesurfer mailing list Freesurfer@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.
