Re: [Freesurfer] Surface area measurement method
Hi, basically, i would like to use the area measure for group analysis, but i'm not sure whether that's ok to do. my questions would be: is it suitable for group analysis? what should i cite if i do? is surface area represented vertex-wise, with a vertex' adjacent face's area added and divided by 3? What happens when resampling to the standard mesh: The method assures that total area (or volume) is preserved when mapping between subjects was that referring to the method described by Winkler or the default FreeSurfer way of doing it? andreas On Wednesday, June 05, 2013 23:22:46 Douglas N Greve wrote: Hi Andreas, it is not the same method but somewhat related. The method assures that total area (or volume) is preserved when mapping between subjects. How much detail do you need? doug On 06/04/2013 05:21 AM, Andreas Berger wrote: Hello FreeSurfers, after reading this [1] paper about measuring surface area, i realized i don't know what the default way of measuring surface area is in FreeSurfer. Is it similar to what's described in the paper? Could you point me to the right documentation or publication? Forgive me if i've overlooked it, i found something for thickness, but not for area. To clarify, i don't mean parcellation-based areas, i mean the measure that i find in /surf/hemi.area. thanks, regards, Andreas [1] Measuring and comparing brain cortical surface area and other areal quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43 ___ 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] OptSeq first time
Hello all, This is my first question in this list and it is about OptSeq2. I am nee to this command. In brief, I wish to insert the following but Some of them I could not handle it: My experiment has three conditions although I will later specify them as one condition: Moving hand at three different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. My design will have two columns : main effect of moving hand and the 1 order. My contrast will be like this [1 0; 0 1] This is what I would like to optimize using OptSeq2: Event design 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this 2) TR 3 3) volumes 150 4) 45 hand movement; 15 at each target level ( I could not do this ) 5) each movement lasts for 3 seconds I am not sure whether I should use null events or the Period between movement is enough. Also my main aim is to optimize the best design in terms of detection. Please any guide or help Thanks AS ___ 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 overlay scale bar background color
you can change it to white via: set scalebar_bright 255 cheers, Bruce On Mon, 10 Jun 2013, Jörg Pfannmöller wrote: Dear FSexperts, the overlay scale bar consists of a colored and a gray part. Unfortunately, the gray in the binary colored represetation of the brain curvature is exactly the same as in the overlay scale bar. Is it possible to change the color in the scale bar background to white? Regards Joerg On Fri, 31 May 2013 16:20:24 -0400 (EDT) Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: mri_normalize is a binary so you can't, just recon-all. On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote: I only find flags for mri_normalize and mri_segment in recon-all, and I have trouble reading the contents mri_normalize with a regular text editor. caspar 2013/5/31 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Caspar it changes some parameters to the intensity normalization and segmentation to account for the lower SNR and increased CNR in the mprage. You'll need to look in the recon-all script for the details cheers Bruce On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote: Hi! Is there more documentation on what settings the mprage flag enables in recon-all? Specifically, I would be interested which individual steps it affects and what the parameters are for each of the steps. Thanks! Caspar 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] Coupling cortical and TRACULA results
Hi list, Thiebaut de Schotten et al., in an article on cortex (Monkey to human comparative anatomy of the frontal lobe association tracts reported that The superior longitudinal fasciculus has three distinct branches (Petrides and Pandya, 1984). In humans, the first branch of the superior longitudinal fasciculus (SLF I) connects to the superior parietal lobule and precuneus (BA 5 and 7), to the superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas (BA 24). The second branch (SLF II) originatesin the anterior intraparietal sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third branch (SLF III) connects the intraparietal sulcus and inferior parietal lobule to the inferior frontal gyrus (BA 44, 45, 47) By TRACULA output we have 2 output SLFp and SLFt. Having also cortical results, I wonder if possible to know which are the seed and target areas of SLF p and SLFt or al least to know which is that branch that is described by SLFp output. 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] volume called 001.mgz
Hi Varghese, is Image1 a dicom file? doug On 6/10/13 10:09 AM, Varghese Chikku wrote: Dear All, I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni freesurfer@freesurfer-VirtualBox:~$ recon-all -i /home/freesurfer/Desktop/10035BL/T1pre/Image1 -autorecon-all -s 10035BLFS Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/10035BLFS mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz file not found or unknown file type for file /home/freesurfer/Desktop/10035BL/T1pre/Image1 # #@# MotionCor Mon Jun 10 16:03:45 CEST 2013 ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/10035BLFS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013 For more details, see the log file /usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting freesurfer@freesurfer-VirtualBox:~$ ___ 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] Coupling cortical and TRACULA results
You can find the aparc+aseg mapped from T1 space to DWI space in the dlabel/diff directory. You can overlay it on the paths reconstructed from tracula to see which aparc+aseg labels the paths overlap with. The identities of the labels in the aparc+aseg are in $FREESURFER_HOME/FreeSurferColorLUT.txt. On Mon, 10 Jun 2013, std...@virgilio.it wrote: Hi list, Thiebaut de Schotten et al., in an article on cortex (Monkey to human comparative anatomy of the frontal lobe association tracts reported that The superior longitudinal fasciculus has three distinct branches (Petrides and Pandya, 1984). In humans, the first branch of the superior longitudinal fasciculus (SLF I) connects to the superior parietal lobule and precuneus (BA 5 and 7), to the superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas (BA 24). The second branch (SLF II) originatesin the anterior intraparietal sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third branch (SLF III) connects the intraparietal sulcus and inferior parietal lobule to the inferior frontal gyrus (BA 44, 45, 47) By TRACULA output we have 2 output SLFp and SLFt. Having also cortical results, I wonder if possible to know which are the seed and target areas of SLF p and SLFt or al least to know which is that branch that is described by SLFp output. 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] Installation trouble on Macbook Air (no such file or directory)
Nate, Try typing the following from the command window: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Or, you can add these lines to your .bashrc file in your home directory by using any text editor, or by typing the following in the command line: echo export FREESURFER_HOME=/Applications/freesurfer ~/.bashrc echo source $FREESURFER_HOME/SetUpFreeSurfer.sh ~/.bashrc Once these lines are in your .bashrc file, freesurfer will load everytime you open the terminal program. -Zeke I am new to Unix and FreeSurfer, and I am having some trouble installing FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just fine, and when I start the installation steps, I'm instructed to add some lines to my .cshrc or .tcshrc files in my home directory. Can anyone point me to this file? Also, just below on the installation dialog, it says for sh or bash users: export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh Can I use these instead of the first two lines of code? I tried to enter these bash lines one at a time into my terminal window. The first one (export) did not give me any errors but for the source one, I received the message: bash: /freesurfer/SetUpFreeSurfer.sh: No such file or directory. Any idea as to why I am getting this error? My apologies in advance for my lack of experience. Many thanks, Nate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] volume called 001.mgz
there are 2 ways to run FS: 1. Specify the input data with -i (usually one slice from a dicom series). 2. Create the subject directory and convert the input volumes to mgz volumes named subject/mri/orig/00[1234].mgz and run recon-all without -i. sounds like you did 2 without the conversion. Easier to just do 1 in general and let recon-all create what it wants cheers Bruce On Mon, 10 Jun 2013, Varghese Chikku wrote: Dear All,I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni freesurfer@freesurfer-VirtualBox:~$ recon-all -i /home/freesurfer/Desktop/10035BL/T1pre/Image1 -autorecon-all -s 10035BLFS Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/10035BLFS mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz file not found or unknown file type for file /home/freesurfer/Desktop/10035BL/T1pre/Image1 # #@# MotionCor Mon Jun 10 16:03:45 CEST 2013 ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/10035BLFS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013 For more details, see the log file /usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting freesurfer@freesurfer-VirtualBox:~$ ___ 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] autorecon3 error
Dear Doug Sorry for late answer. I did open as: tksurfer qsm1_17 lh inflated, and then File load surface lh.sphere.reg and tksurfer qsm1_17 lh sphere.reg Neither of them look bad, it looks very spherical, an has nothing strange to my eyes... Any other ideas??? Best Regards Gabriel - Mensaje original - De: Bruce Fischl fis...@nmr.mgh.harvard.edu Fecha: Jueves, 6 de Junio de 2013, 6:16 pm Asunto: Re: [Freesurfer] autorecon3 error A: Gabriel Gonzalez Escamilla ggon...@upo.es CC: freesurfer@nmr.mgh.harvard.edu Hi Gabriel seems like something is wrong with that surface file. Can you load the lh.sphere.reg in tksurfer and see if it looks ok? Bruce On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote: Dear Freesurfers I am running an autorecon3 to the same subject that Rafa sent you (the name looks different but is exactly the same subject), with the command to fix the ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but now is encountering the following error, this time seems to be something with the seg.mgz. #- #@# Cortical Parc lh Thu Jun 6 17:01:26 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 qsm1_17 lh ../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ f[113526]-v[1] = 539832625 - out of range! reading atlas from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all -s qsm1_17 exited with ERRORS at Thu Jun 6 17:01:33 CEST 2013 For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas how to fix this? Bests, Gabriel ___ 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. font size=3--br /PhD. student Gabriel González-Escamillabr /Laboratory of Functional Neurosciencebr /Department of Physiology, Anatomy, and Cell Biologybr /University Pablo de Olavidebr /Ctra. de Utrera, Km.1br /41013 - Sevillebr /- Spain -br /br /Email: ggon...@upo.esbr /http://www.upo.es/neuroaging/es//font ___ 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] AR2 Error
Copy this file to $FREESURFER_HOME/bin/mri_segstats ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard doug On 06/07/2013 06:01 PM, Erin Browning wrote: The last thing I ran was recon-all -s freesurfer -autorecon2 -autorecon3 Which still failed. We quality check after ar1, so we need to run ar1 separately from ar2 and 3. On Jun 7, 2013 4:53 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: you need to include the -autorecon3 flag simultaneously with the -autorecon1 and -autorecon2 flags. On 06/07/2013 05:45 PM, Erin Browning wrote: It fails before ar3 runs. On Jun 7, 2013 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: There is no indication in this log file that you ran autorecon3 doug On 06/07/2013 02:51 PM, Erin Browning wrote: Here's the log. I ran mri_add_xform_to_header after it failed again last time and am currently rerunning AR2+3 on it, so you can probably ignore the latest modifications to it. http://gate.nmr.mgh.harvard.edu/filedrop2/?p=iowkgmv We're running Mac OSX 10.6.8. Thanks, Erin On Fri, Jun 7, 2013 at 12:22 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hmmm, I don't know. I think that something strange is happening. Can you send me the new recon-all.log file? Also, tell me what platform you are using and I'll send you a new version of mri_segstats doug On 06/07/2013 01:14 PM, Erin Browning wrote: Could it be that since we skip motioncor, we skip the mri_add_xform_to_header program as well? Should I be running that separately? Thanks, Erin Browning On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu mailto:brown...@uwm.edu wrote: Hi Doug-- Running: recon-all -s freesurfer -autorecon2 -autorecon3 produced the same error. Could you send me the new version of the program? Thanks! Erin Browning On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: OK, this is a known problem when running recon-all with -autorecon1 -autorecon2 but not autorecon3. If you run it with -autorecon3, then it
Re: [Freesurfer] surface stream steps
The classification of WM probably takes the most. This includes a lot of things, the longest is the subcortical segmentation. See recon-all-status.log for a list of times of each operation. doug On 06/08/2013 03:05 PM, Joshua Lee wrote: Dear Freesurfers, From the Wiki Freesurfer surface stream follows something like: 1. Affine registration to Tal. 2. Bias correction and skull stripping 3. Classify WM 4. Cut hemisphere planes 5. Tile WM surface 6. Refine WM surface following GM-WM intensity gradients 7. Nudge (nudge?) WM surface to follow the GM-CSF gradient to generate pial surface 8. Labeling Data Set 9. Stats May I ask which couple of these steps tend to be the most computationally taxing/longest to complete? Also, I'm not sure I understand #7. Is the WM surface scaled in some sense to approximate the GM-CSF boundary, or is this just a refinement step like #6 of a surface that already approximates the GM-CSF boundary? Thanks, I've spent most of my time working with the sub-cortical stream. - Joshua ___ 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] Surface area measurement method
On 06/10/2013 02:18 AM, Andreas Berger wrote: Hi, basically, i would like to use the area measure for group analysis, but i'm not sure whether that's ok to do. my questions would be: is it suitable for group analysis? yes what should i cite if i do? We don't have a citation specifically for it. It is used by this paper, but it does not describe it in detail. Greve, D. N., Van der Haegen, L., Cai, Q., Stufflebeam, S., Sabuncu, M. R., Fischl, B., Brysbaert, M. (2013). A Surface-based Analysis of Language Lateralization and Cortical Asymmetry. /Journal of cognitive neuroscience/, (Early Access), 1-16. is surface area represented vertex-wise, with a vertex' adjacent face's area added and divided by 3? That is how the ?h.area file is created. What happens when resampling to the standard mesh: The method assures that total area (or volume) is preserved when mapping between subjects was that referring to the method described by Winkler or the default FreeSurfer way of doing it? No, his way is more elaborate and probably much better but harder to implement and slower. The currently implemented version effectively preserves area over any given patch when mapping to fsaverage. I don't know what the size of the patch is but is probably on the order of 5mm (probably smaller). doug andreas On Wednesday, June 05, 2013 23:22:46 Douglas N Greve wrote: Hi Andreas, it is not the same method but somewhat related. The method assures that total area (or volume) is preserved when mapping between subjects. How much detail do you need? doug On 06/04/2013 05:21 AM, Andreas Berger wrote: Hello FreeSurfers, after reading this [1] paper about measuring surface area, i realized i don't know what the default way of measuring surface area is in FreeSurfer. Is it similar to what's described in the paper? Could you point me to the right documentation or publication? Forgive me if i've overlooked it, i found something for thickness, but not for area. To clarify, i don't mean parcellation-based areas, i mean the measure that i find in /surf/hemi.area. thanks, regards, Andreas [1] Measuring and comparing brain cortical surface area and other areal quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43 ___ 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] OptSeq first time
Hi, can you at least come up with an optseq2 command line that I could then help you with? There are lots of examples on the web page. You should be able to get to a point where you have an error. thanks doug On 06/10/2013 05:14 AM, fMRI wrote: Hello all, This is my first question in this list and it is about OptSeq2. I am nee to this command. In brief, I wish to insert the following but Some of them I could not handle it: My experiment has three conditions although I will later specify them as one condition: Moving hand at three different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. My design will have two columns : main effect of moving hand and the 1 order. My contrast will be like this [1 0; 0 1] This is what I would like to optimize using OptSeq2: Event design 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this 2) TR 3 3) volumes 150 4) 45 hand movement; 15 at each target level ( I could not do this ) 5) each movement lasts for 3 seconds I am not sure whether I should use null events or the Period between movement is enough. Also my main aim is to optimize the best design in terms of detection. Please any guide or help Thanks AS ___ 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] HypoIntense Lesions
Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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] HypoIntense Lesions
Hi Panos sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know cheers Bruce On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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] HypoIntense Lesions
Hi Panos, not in an SWI scan. The aseg.stats file created by recon-all will give you WM hypointensities based on the T1. doug On 06/10/2013 11:50 AM, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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] white matter volume per lobe...
Hi Gonzalo, the segmentation that you are seeing is paired with the insula parcellation. doug On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote: Hi Doug: The command is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200 and the terminal output is: mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200 SUBJECTS_DIR /usr/local/freesurfer/subjects subject OAS1_0001_MR1 outvol mri/lobulitos_2.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 200.00 RipUnknown 1 Reading lh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white Reading lh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial Loading lh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Reading rh white surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white Reading rh pial surface /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial Loading rh annotations from /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot reading colortable from annotation file... colortable with 8 entries read (originally none) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz Loading filled from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7659 vertices from left hemi Ripped 7544 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz ASeg Vox2RAS: --- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; - Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931 Used brute-force search on 139 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to mri/lobulitos_2.mgz Sincerely, Gonzalo Rojas Costa On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: can you send me your full command line as well as the terminal output? On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote: Hi Doug: But, in the mri_aparc2aseg command, I test with the --wmparc-dmax 200 option... I put that big value to test it, but I got the image that I sent you... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl -- 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
Re: [Freesurfer] HypoIntense Lesions
Hi Doug and Bruce, Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them? In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)? Thanks for your help, Panos From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know cheers Bruce On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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] HypoIntense Lesions
On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote: Hi Doug and Bruce, Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them? This is already done in recon-all (aseg.mgz and aseg.stats) In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)? That is not output by default, but you can get it relatively easily in two steps: mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77 -- This creates a binary image Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and volume of each lesion will be in the summary file doug Thanks for your help, Panos From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know cheers Bruce On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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 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] OptSeq first time
Correction This is the lats code : optseq2 --ntp 140 --tr 3 --psdwin 6 15 3 --ev ev20 3 20 --ev ev40 3 20 --ev ev60 3 20 --nkeep 3 --o OptSeq_TRIALS/trial_squ --nsearch 1 So The duration is 3 seconds for each and each repeat it 20 times. What I need is to change/add the ISI to be 7 + or - 1.5 seconds. Any help please ? Another point is about the psdwin, I am not sure what exactly it represents. I saw your slides but I thought this should also change the ISI,. Can you comment on it please ? Thanks AS On Mon, Jun 10, 2013 at 5:49 PM, fMRI fmri2...@gmail.com wrote: Dear Prof Douglas, Thanks for your response. I managed to do the following: optseq2 --ntp 140 --tr 3 --padwin 0 12 3 --ev ev15 --ev ev30 --ev ev45 --nkeep 3 --o trial --nsearch 1 Now what I really want to do is to make the ISI 7 seconds + or - 1.5 seconds. I am not sure how I should use the percentage option if this is what I should change plus the ISI time? I hope this clarifies it more Regards, AS On 10 Jun 2013, at 16:21, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi, can you at least come up with an optseq2 command line that I could then help you with? There are lots of examples on the web page. You should be able to get to a point where you have an error. thanks doug On 06/10/2013 05:14 AM, fMRI wrote: Hello all, This is my first question in this list and it is about OptSeq2. I am nee to this command. In brief, I wish to insert the following but Some of them I could not handle it: My experiment has three conditions although I will later specify them as one condition: Moving hand at three different target level ( say 10 20 30). Then I will model them as a one condition and enter the parametric response as a first order polynomial effects. My design will have two columns : main effect of moving hand and the 1 order. My contrast will be like this [1 0; 0 1] This is what I would like to optimize using OptSeq2: Event design 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this 2) TR 3 3) volumes 150 4) 45 hand movement; 15 at each target level ( I could not do this ) 5) each movement lasts for 3 seconds I am not sure whether I should use null events or the Period between movement is enough. Also my main aim is to optimize the best design in terms of detection. Please any guide or help Thanks AS ___ 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.
[Freesurfer] Hippocampal subfields intensity
Hi, Freesurfer Experts After usual processing with recon-all -all we get the aseg.stats file with several data including intensity values like: normMean normStdDev normMin normMax normRange Left-Hippocampus 77.8939 7.574846. 105.59. How could I get similar results for each hippocampal subfield, assuming I also generated all posterior*.mgz files corresponding to each subfield? I guess I should first binarize each of the subfields file with a threshold=127 to map all the pertinent voxels, and then use these files as masks over nu.mgz and calculate the intensities values. But I do not know the best way to accomplish this after the binarize step. Thank you in advance for any help. Marcos ___ 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 intensity
Hi Marcos, the right way of doing this is using the soft posteriors to compute the mean and variance, rather than thresholding at p=0.5. For instance, if you wanted to compute the mean and variance of the intensitites of the subiculum, you would do something like this: mean=sum(Ps.*NU)/sum(Ps); variance=sum(Ps.*(NU-mean).^2)/sum(Ps); (where Ps is the posterior of the subiculum) Cheers, /Eugenio On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote: Hi, Freesurfer Experts After usual processing with recon-all -all we get the aseg.stats file with several data including intensity values like: normMean normStdDev normMin normMax normRange Left-Hippocampus 77.8939 7.574846. 105.59. How could I get similar results for each hippocampal subfield, assuming I also generated all posterior*.mgz files corresponding to each subfield? I guess I should first binarize each of the subfields file with a threshold=127 to map all the pertinent voxels, and then use these files as masks over nu.mgz and calculate the intensities values. But I do not know the best way to accomplish this after the binarize step. Thank you in advance for any help. Marcos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] How to measure the surface dimension in a mask image after mri_glmfit?
Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ 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] HypoIntense Lesions
Hi Doug, Thanks for your response, it was really helpful. In addition to the previous comments, I have some subjects that have a hematoma that is not shown in the aseg.mgz file, and hence is not shown as a hypointense cluster after doing the analysis provided below. Do you know if there is any other way to extract information (such as outlining it and/or acquiring its volume) about something like? Thanks again, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 12:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote: Hi Doug and Bruce, Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them? This is already done in recon-all (aseg.mgz and aseg.stats) In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)? That is not output by default, but you can get it relatively easily in two steps: mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77 -- This creates a binary image Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and volume of each lesion will be in the summary file doug Thanks for your help, Panos From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know cheers Bruce On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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 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] HypoIntense Lesions
Hi Panos, I don't know an automatic way to do it. You could label it by hand on tkmedit or freeview. doug On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote: Hi Doug, Thanks for your response, it was really helpful. In addition to the previous comments, I have some subjects that have a hematoma that is not shown in the aseg.mgz file, and hence is not shown as a hypointense cluster after doing the analysis provided below. Do you know if there is any other way to extract information (such as outlining it and/or acquiring its volume) about something like? Thanks again, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 12:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote: Hi Doug and Bruce, Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them? This is already done in recon-all (aseg.mgz and aseg.stats) In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)? That is not output by default, but you can get it relatively easily in two steps: mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77 -- This creates a binary image Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and volume of each lesion will be in the summary file doug Thanks for your help, Panos From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know cheers Bruce On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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 -- 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] Set Up question
Hi David, it is not a problem if you're not going to run FS-FAST. If it
bugs you, you can
setenv NO_FSFAST 1
in your cshrc file prior to sourcing the FS env
doug
On 06/10/2013 03:35 PM, David Dalton wrote:
Hello FreeSurfer experts,
I recently downloaded and installed FreeSurfer on my Mac computer, but
I have a few questions about the startup.
1. When I run FreeSurfer, I get the following. I know the Wiki says
to ignore the warning, and FreeSurfer does run normally after this,
but I wanted to be sure it really was not a problem.
[SiriasBook:/] csirias% setenv FREESURFER_HOME Applications/freesurfer/
[SiriasBook:/] csirias% source Applications/freesurfer/SetUpFreeSurfer.csh
freesurfer-Darwin-lion-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME Applications/freesurfer/
FSFAST_HOME Applications/freesurfer//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR Applications/freesurfer//subjects
WARNING: The /Users/csirias/matlab/startup.m file does not appear to be
configured correctly. You may not be able
to run the FS-FAST programs
Try adding the following lines to /Users/csirias/matlab/startup.m
-cut-
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
-cut-
MNI_DIR Applications/freesurfer//mni
[SiriasBook:/] csirias%
2. When I type in 'freeview' to the command line, I get several other
messages as the program opens. I am not sure if they are a problem,
but here they are. I seem to be able to run freeview despite these
messages, but some others have told me that these messages do not
appear on their computers, so I am wondering why they appear.
[SiriasBook:/] csirias% freeview
2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable
3. And my last question. How do I run FreeSurfer automatically when I
open the terminal window? I would like to just type 'freeview' into
the command line to have the program run, but I currently have to type
setenv FREESURFER_HOME Applications/freesurfer/
followed by
source Applications/freesurfer/SetUpFreeSurfer.csh
in order for the program to run.
Thank you so much for any help you can give! Like I said, the program
appears to run normally despite the messages, but I just want to know
why they are appearing. The last question is more of a convenience issue.
Thanks,
David
___
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] Neuroinformatics Database (NIDB) 4.2.0 released
This is an announcement that Neuroinformatics Database version 4.2.0 has been released. This version includes many performance enhancements and new features. There is also a demo server available with some sample MR data and the ABIDE dataset hosted for users who want to test the database without needing to install it locally. General features: * store any binary or text data, including MR (any dicom modality), EEG, SNP, video, audio, images, etc. * store assessment/clinical measure values (DSM code, etc, only values, not full assessments) * real-time QC for MR data, with values stored in the database * automatic pipeline processing of any image data, with results stored in the database * query and retrieve any of the above data and dump to local/remote FTP, NFS share, or export in NiDB format * additionally: DICOM receiver, store family pedigree information, store MR behavioral data, download stats, reports New features: * sharing of imaging data between NiDB instances, while maintaining anonymity and eliminating subject duplication * improved pipelines: testing mechanism for new pipelines, creating/editing scripts, and second level pipelines * query performance improved on pipeline results: 4.4 million result values retrieved in 107 seconds. * methods for creating new back-end NiDB modules Download version 4.2.0 in .tar.gz format or VirtualBox VM: http://nidb.sourceforge.net. We'll be presenting at HBM in Seattle next week, so stop by! NiDB is developed by and with support from the Olin Neuropsychiatry Research Center at Hartford Hospital/Institute of Living. ___ 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] HypoIntense Lesions
Great, thank you! Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 3:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos, I don't know an automatic way to do it. You could label it by hand on tkmedit or freeview. doug On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote: Hi Doug, Thanks for your response, it was really helpful. In addition to the previous comments, I have some subjects that have a hematoma that is not shown in the aseg.mgz file, and hence is not shown as a hypointense cluster after doing the analysis provided below. Do you know if there is any other way to extract information (such as outlining it and/or acquiring its volume) about something like? Thanks again, Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 12:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote: Hi Doug and Bruce, Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would work great as well. Do you know where I could look for them? This is already done in recon-all (aseg.mgz and aseg.stats) In addition, Doug besides the WM hypointensities in the aseg.stats is there something that shows the number of lesions, instead of the volume (or the volume that corresponds to each lesion)? That is not output by default, but you can get it relatively easily in two steps: mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77 -- This creates a binary image Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and volume of each lesion will be in the summary file doug Thanks for your help, Panos From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, June 10, 2013 11:52 AM To: Fotiadis, Panagiotis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] HypoIntense Lesions Hi Panos sorry, forgot to respond to this. We have tools for labeling hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It might work on those if you also had a good T1 and some training data. Doug might know cheers Bruce On Mon, 10 Jun 2013, Fotiadis, Panagiotis wrote: Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos ___ 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 -- 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 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] How to measure the surface dimension in a mask image after mri_glmfit?
Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ 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] Hippocampal subfields intensity
Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
(reslice like):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio
On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
Hi, Eugenio
TY for your fast help. I understood you were suggesting to compute
that on MatLab and I tried this:
NU=MRIread('nu.mgz')### that runs ok
Ps=MRIread('posterior_left_subiculum.mgz') ### it fails with the
following message
WARNING: error reading MR params
Attempted to access mr_parms(1); index out of bounds because
numel(mr_parms)=0.
Error in MRIread (line 100)
tr = mr_parms(1);
I solved creating a little customized nMRIread.m with the following
changes:
if numel(mr_parms) 0
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
else
mr_parms(1) = 0;
mr_parms(2) = 0;
mr_parms(3) = 0;
mr_parms(4) = 0;
tr = mr_parms(1);
flip_angle = mr_parms(2);
te = mr_parms(3);
ti = mr_parms(4);
end
With those changes I assigned 0 to mr-parms elements so it runs
without errors
But whe I tried the following line I copy and pasted from your
message:
mean=sum(Ps.*NU)/sum(Ps); ### I got the following error
Undefined function 'times' for input arguments of type 'struct'.
Any help?
Cheers, Marcos
PS: I promised I will post the final solution to list. But I guess it
is more didactic if these little problems are solved before.
TY, again.
Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu:
Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio
On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
Hi, Freesurfer Experts
After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus 77.8939 7.574846.
105.59.
How could I get similar results for each hippocampal subfield,
assuming I also generated all posterior*.mgz files corresponding to
each subfield?
I guess I should first binarize each of the subfields file with a
threshold=127 to map all the pertinent voxels, and then use these
files as masks over nu.mgz and calculate the intensities values. But I
do not know the best way to accomplish this after the binarize step.
Thank you in advance for any help.
Marcos
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Re: [Freesurfer] Fwd: problem about file format
Thanks. I now find that, when I copy (or cut) the re-con folder from SUBJECTS_DIR to the shared folder (with XP), it seems that no changes happen - the file format remains the same. But if I restart the Xubuntu, and copy (or cut) this re-con folder from shared folder back to SUBJECTS_DIR, then the file format automatically changes and the re-con results can not be recognized. This is quite odd... I have to move the re-con results to the shared folder because in the Xubuntu FSV5.1.0 virtual hard disk the space is only 10G. So to me now, if I can expand the disk to, say for example, 50G, then at least I don't need to move the re-con results but just save them in SUBJECTS_DIR, and so the file formats will not change. On 7 June 2013 20:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I meant for you to cat them and put them in the text of the email. Something is badly wrong with them. They should be simple text files with a 4x3 matrix and a couple of header lines. Not sure what happened but you will need to delete them and regenerat them cheers Bruce On Fri, 7 Jun 2013, huang bs wrote: Seems that I can not post the attachements... -- Forwarded message -- From: huang bs huan...@gmail.com Date: 5 June 2013 22:51 Subject: Re: [Freesurfer] problem about file format To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Dear Bruce, Yes, sure. I printed the screens and showed you two cases. One can be recognized, the other one can not. Please find attached for the six figures. I also attached the files talairach.xfm and talairach.auto.xfm for the subject linziyi. One more question: how to extend the hard disk space in Xubuntu, especially in the folder /home/virtualuser/freesurfer/**subjects ? If possible, I don't want to move the data to the shared folder and then face such problem. Sorry I am quite new to Linux so some questions may be quite stupid. Thank you very much! On 05/06/2013, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/**subjects/linziyi/mri/** transforms/talairach.xfm and send us the contents? Bruce On Wed, 5 Jun 2013, huang bs wrote: Hi All, Sorry to take up your time. My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/**subjects/linziyi/mri/** transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as executable file. That's quite strange because I did not make such change to it. These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either. For the cases I just re-con, since they are not moved to elsewhere, everything seems OK. Have you guys had such problem before and how to fix it? Thanks! -- Best Regards, B Huang 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/**compliancelinehttp://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. -- Best Regards, Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong -- Best Regards, Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong -- Best Regards, Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong ___ 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] How to measure the surface dimension in a mask image after mri_glmfit?
It's --sum for this, not --o doug On 6/10/13 4:44 PM, Glen Lee wrote: Thanks Doug! I just tried, but I got an error: mri_segstats --seg mask.mgh --id 1 --i /fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat ERROR: Option --o unknown I don't see --o option when I looked up mri_segstats --help either. FYI, I'm using v5.1. Any idea? On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Glen, you can use mri_segstats --seg mask.mgh --id 1 --i $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat doug On 06/10/2013 03:17 PM, Glen Lee wrote: Dear freesurfer users I'm wondering if there is any way of figuring out the surface size within a mask image (mask.mgh) which is generated after running a group-level GLM analysis (2nd RFX) using mri_glmfit. As I'm thinking, this may be: number of vertex by dimension of one vertex (1mm). But I could be wrong and let me know if anyone knows the solution. -Glen fyi) the group analysis was performed in freesurfer sym space. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
