[Freesurfer] Amygdala subfields
Dear all, is the amygdala subfields segmentation available or you are working on it? Thanks, Stefano ___ 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] Amygdala subfields
Hi Stefano, we are working on an algorithm to segment the nuclei, but unfortunately I do not think it is going to be released any time soon. Kind regards, /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: std...@virgilio.it To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, November 24, 2014 3:42:05 AM Subject: [Freesurfer] Amygdala subfields Dear all, is the amygdala subfields segmentation available or you are working on it? Thanks, Stefano ___ 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
[Freesurfer] Creat ROI from annotation file
Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder. I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture). Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter. Could anyone help me creat good masks? Thanks a lot! Zhiwei ___ 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] Regarding recon-all
sorry, I think =5 is in brain On Mon, 24 Nov 2014, Gunjan Gautam wrote: Hi Bruce, What about the voxels having value equal to 5 (if exists) ? Gunjan On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam gunjan.gemin...@gmail.com wrote: Ok thank you Bruce On Nov 23, 2014 10:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: we don't have a binary one, but all voxels in brainmask.mgz that are 5 are in brain and everything 5 is not in brain cheers Bruce On Sun, 23 Nov 2014, Gunjan Gautam wrote: Thanks, And what about the binary brain mask? I am able to see only the stripped volume but need the binary brain mask as well. Gunjan On Nov 23, 2014 8:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan 15 min is about what it is going to take. You could do it faster but then the failure rate would go up. We've tuned it to improve automaticity and reduce failures quite a bit. cheers Bruce On Sat, 22 Nov 2014, Gunjan Gautam wrote: Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the stripped brain and its binary mask. I also need to ask, which file of the output (name with extension) is the binary brain mask ? Best regards, Gunjan ___ 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. ___ 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
Re: [Freesurfer] Tracula_critical issue
Dear Anastasia, Thank you very much for your answer. In my analysis I have two groups 23 patients and 27 controls. My problem right now is that this change in the results (from the output of trac-all -path -c) gave me different P values between the groups, sometimes the results are significant and sometimes it is not! Till today I repeated this analysis many times and I collected the results after 5 consecutive runs (all the tracts for all the subjects) Recently and In order to find a solution for this problem I used the following command line to generate the mean metrics and the tracts volume: fslstats - dti_FA.nii.gz -k path.pd_bin.nii.gz -M -V [ I binarized path.pd.nii.gz (the output of trac-all -path -c for every tract) using fslmaths path.pd.nii.gz -thr 0.999 path.pd_bin.nii.gz and I used this treashold to make my mask conservative as possible] In this case I got stable numbers. i.e when I run this command line again the results are the same. Kindly is this valid? can I use fslstats instead of the third step in Tracula trac-all -path -c to calculate the mean metrics and the tract's volume? Also what is the difference between fslstats and trac-all -path -c (technically) I highly appreciate your support Mohamad From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Friday, November 21, 2014 5:10 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula_critical issue Hi Mohamad - As it's a probabilistic method that's sampling from a distribution, there is a bit of randomness built in (which should decrease as you increase the number of samples that you collect). You'll find that the the weighted average measures are the most reliable, as they are less affected by the tails of the distribution. a.y On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote: Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file pathstats.overal.txt regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three pathstats.overal.txt files for the same subject after three consecutive runs for the trac-all -path -c (the same subject) Looking forward for your support Thanks ___ 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] tksurfer curvature and overlay displays
Hi Graham have you tried freeview? We stopped development on the tktools some time ago. cheers Bruce On Fri, 21 Nov 2014, Graham Wideman wrote: Hi all, I'm having some issues (some possibly mine, some possibly tksurfer's) getting tksurfer (5.3c6) to display curvature the way I think it should be able to. I am using the bert sample data. The Curvature display - If I use the Show Curvature button in the UI control panel, I get the familiar gyrus=green; sulcus=red pattern applied to the displayed brain. The Configure Curvature Display is a bit of a shambles, and I think should be fixed. First, it is virtually impossible to set midpoint using the slider, because the values it pushes to the adjacent textbox are way too coarse. Typing values into the midpoint textbox works, in that it affects the balance of red and green in the display. However the textbox does not affect the position of the slider, suggesting that it actually does not work. That said, there's no actual adjustment of the threshold size. Indeed, it's not clear that there actually IS a threshold -- perhaps there isn't. Maybe threshold midpoint just sets the midpoint of the color range? And then there's a a textbox labeled threshold slope. I'm pretty sure that's nonsensical phrase. What this box appears to do is set the ratio of color to curvature value. Ie: Color intensity. Bottom line -- this dialog only partially fits the purpose at hand, and is so confusingly wording that ones attempts to use it are pretty much random. It may even be that some UI elements or functionality that was once there has gone missing accidentally? Finally, I wanted a colorbar for the curvature display, and so far as I can tell there isn't one. I can turn on a colorbar, but it's the one for overlays. Using a Curvature variable as an overlay I next tried to read in the k1.crv variable as an overlay. This sort of works, but gives a very mottled display (except using heat map color scheme), I think because even in definite sulcus and gyrus regions, the curvature values straddle the border of the grey range of color, and I'm not sure how to adjust it sensibly. -- I couldn't figure out how to set the overall color range, that is to say the extremes of the colorbar. These seem stubbornly stuck at 5.0 and -5.0. In particular, the Theshhold Max setting doesn't seem to affect the extremes of the color range. -- I couldn't figure out how to eliminate the large grey range in the middle of the color range. I noted that the Threshhold Min setting can be used to make the grey range larger, but setting Min below 1.5 (for example, zero) does not eliminate the grey between 0 and +/-1.5. Anybody have any helpful clues on these items! Thanks! -- Graham ___ 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] prefrontal cortex label
What is the full terminal output and error msg? On 11/21/2014 04:14 AM, Anna Jonsson wrote: hi, I have tried to make prefrotnal cortex label by doing first mri_annotation2label --subject $subject --hemi rh --outdir $subject/label mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/lh.prefrontalcortex.label $subject lh pial | grep thickness left_prefrontal i get error and say it cant find label. any pointers on what im doing wrong? thank you ___ 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] mri_glmfit-sim sim-sign
Have you looked at mri_glmfit-sim --help On 11/21/2014 01:51 PM, Jon Alan Wieser wrote: hi please explain the differece between --sim-sign abs, neg, and pos ___ 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] seed-based fcMRI analysis between thalamus and cortex
I have not read that paper, but I think it can do what you want. Have you seen? http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough On 11/22/2014 11:55 AM, std...@virgilio.it wrote: Dear all, is FS-FAST able to perform seed-based fcMRI analysis between thalamus and cortex (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852505/)? Thanks for your work, Stefano ___ 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] Resample the surface mesh
Would mris_decimate work? On 11/24/2014 01:53 AM, 婷 wrote: Thanks for your reply with detailed explanation. I am interested in what if we apply analysis on native surface first. Still wondering:) Ting On Nov 23, 2014, at 8:23 PM, Thomas Yeo ytho...@csail.mit.edu wrote: Hi Ting, What I usually do is to project my functional data to fsaverage space and then smooth and downsample to whatever resolution I want. There are different fsaverage resolution meshes, like fsaverage5 (~20k vertices) and fsaverage6 (~80k vertices). This can be achieved using standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note that in this scenario, even though the data is in fsaverage space, this does not preclude individual subject analysis. The advantage of the above approach is that we can still easily perform a group analysis if we want to in the future. The disadvantage is that we lose a little bit of the subject's native cortical geometry, which is not an issue for your proposed approach. However, I am not aware of freesurfer tools that will let you downsample an arbitrary mesh. Perhaps someone who is more intimately aware of freesurfer's tools can jump in on this. Cheers, Thomas On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutin...@gmail.com wrote: Hi Thomas, I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas? Thanks, Ting On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ytho...@csail.mit.edu wrote: Hi Ting, I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister. Cheers, Thomas On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutin...@gmail.com wrote: Dear freesurfer experts, Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer? Many thanks, Ting ___ 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 ___ 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
Re: [Freesurfer] Creat ROI from annotation file
Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the aparc annot. You can look in the recon-all.log file for the command line (just make sure to change the output file name too so that you don't overwrite aparc+aseg.mgz) doug On 11/24/2014 07:54 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder. I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture). Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter. Could anyone help me creat good masks? Thanks a lot! Zhiwei ___ 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] Group analysis
There are two things that are considered. One is the tesselation which smoothing is one. The other is the registration that is used. Using -target Something only specifies the smoothing target (if doing smoothing in mris_preproc). If you want to spec a registration target, you need to first run make_average_subject (which looks like you have done). Second, you need to run surfreg for each subject specifying your average subject with --t. This will create ?h.MyAverage.sphere.reg in each subject's surf folder. Then run mris_preproc with --surfre MyAverage.sphere.reg doug On 11/13/2014 05:06 AM, Roberta Santoro wrote: Dear all, I created an average subject from my dataset and I would like to use it to run a group analysis of thickness. I am using the command: recon-all -s subjid -qcache -target MyAverage When looking at the terminal, I noticed that the srcsurfreg and the trgsurfreg are both sphere.reg: shouldn’t one of the two be sphere.reg.MyAverage? Otherwise, how is the alignment achieved? Thanks for your help. Best, Roberta ___ 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] multiple comparisons correction for individual hemispheres (native space)
Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM, Milde, Christopher wrote: Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, Christopher ___ 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] pial mask
Dear all, After running the recon-all on a subject, I needed to create a 'pial' surface to include the hippocampi, which are not included well in the pial reconstruction. So I generated a mask and used it to mask brain.mgz. 1. All well, except that in both the mask and the masked brain volume (readybrain.mgz, see below), the fill extends with a variable layer of about 1 voxel) above the pial red contour in some areas (see the top, leading me to believe that the red contours we use when editing are not the actual pial surfaces, but some interpolations of the actual calculated pial surface. If this is true, then there may be some editing errors when using these contours. Another explanation could be the resolution of the mris_fill. Please let me know which is the case, and how to fix it so that the mask closely follows the red contour. 2. I need to generate a surface from readybrain.mgz, preferably that can be registered to the sphere.reg and on which cortical parcellation (DK atlass) can be applied. Is there a way? If not, I would still like to know how to generate the surface of this volume. Thank you, Octavian Here is the code I used: cd /usr/local/fs5.3/freesurfer/subjects/subjid mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz \ mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz \ mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz \ cd ./mri \ mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14 --match 17 --match 18 --match 19\ --match 25 --match 31 --match 44 --match 48 --match 49 --match 53 --match 54 --match 55 --match 57\ --match 63 --match 86 --match 96 --match 97 --match 105 --match 106 --match 114 --match 115\ --match 195 --match 199 --match 203 --match 204 --match 205 --match 216 --match 222 --match 225\ --match 507 --match 557 --match 1200 --match 1201 --match 1205 --match 1206 --match 2200 --match 2201\ --match 2205 --match 2206 --o hippoamy.mask.mgz \ fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz \ mri_convert brain.mgz brain.float.mgz -odt float \ mri_mask brain.float.mgz epimask.mgz readybrain.mgz ___ 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] can I apply freesurfer significant clusters as ROI in fMRI study?
What do you mean apply it to your functional data? Analyzed fMRI? In what package? In what space is the fMRI? On 11/20/2014 08:01 AM, chenchunhuichina wrote: Dear freesurfer experts, I searched on the wiki but can not figure out how to solve this problem: I found some significant clusters on graymatter thickness, how can I use it as a ROI in my functional MRI study? I have both structure and function data of the same subjects, so I can either do it in stardard space or native space one by one if possible. Any help is appriciated~ Best 2014-11-20 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ 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] Download of latest Tracula version not possible
Hi all, I am trying to download the latest version of Tracula from this site http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. This seems not to be possible at the moment. Are there server problems? Thanks, Janosch ___ 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] Creat ROI from annotation file
It works! Thanks, Doug. At 2014-11-25 01:19:13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the aparc annot. You can look in the recon-all.log file for the command line (just make sure to change the output file name too so that you don't overwrite aparc+aseg.mgz) doug On 11/24/2014 07:54 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder. I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic.nii --subject fsaverage --hemi lh --identity The parcellation in output volume were like some lines located at the boundry of white matter , and did not cover the gray matter (see picture). Then, I used another methods as follows. Firstly, I converted the annotation file into some label files using mri_annotation2label command; Secondly, I created ROIs using these labels by mri_vol2roi. However, the masks also couldn't cover the gray matter. Could anyone help me creat good masks? Thanks a lot! Zhiwei ___ 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] Resample the surface mesh
It works! Thank you, Doug. Ting On Nov 24, 2014, at 12:17 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Would mris_decimate work? On 11/24/2014 01:53 AM, 婷 wrote: Thanks for your reply with detailed explanation. I am interested in what if we apply analysis on native surface first. Still wondering:) Ting On Nov 23, 2014, at 8:23 PM, Thomas Yeo ytho...@csail.mit.edu wrote: Hi Ting, What I usually do is to project my functional data to fsaverage space and then smooth and downsample to whatever resolution I want. There are different fsaverage resolution meshes, like fsaverage5 (~20k vertices) and fsaverage6 (~80k vertices). This can be achieved using standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note that in this scenario, even though the data is in fsaverage space, this does not preclude individual subject analysis. The advantage of the above approach is that we can still easily perform a group analysis if we want to in the future. The disadvantage is that we lose a little bit of the subject's native cortical geometry, which is not an issue for your proposed approach. However, I am not aware of freesurfer tools that will let you downsample an arbitrary mesh. Perhaps someone who is more intimately aware of freesurfer's tools can jump in on this. Cheers, Thomas On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutin...@gmail.com wrote: Hi Thomas, I want to analyze the data in native surface space. The functional volume data could be register to native surface with bbregister, however, the resolution of the native surface is quite high, too much nodes for computational capacity to me. Any ideas? Thanks, Ting On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ytho...@csail.mit.edu wrote: Hi Ting, I am not an expert, but why do you want to downsample the native surface mesh? The usual way of doing this is to register the full surface mesh with the functional volume data using Doug's bbregister. Cheers, Thomas On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutin...@gmail.com wrote: Dear freesurfer experts, Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer? Many thanks, Ting ___ 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 ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tracula mri_convert error
Hi experts, I wanted to play with Tracula. Strangely, already the first preprocessing step, i.e., conversion to .nii.gz, fails. Apparently, mri_convert (falsely) recognizes my dicom files as MGH dicoms (This looks like an MGH DTI volume). Could this be the reason why it fails? Thanks, Janosch ___ 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.
