Re: [Freesurfer] Repost: Converting BV ROIs to FS
Hi Katie you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point xtal ytal ztal cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie 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] repeated measures ANOVA with two groups
Hi Shannon, sorry for the delay. There are several ways you can do this. If you already have a slope for each subject, then just use that as input and use the simple two group FSGD file. If you really want to do the RM ANOVA, then there are two ways. The simpler way is to create a stack of all subjects for each visit (eg, v1, v2, and v3) using mris_preproc. Next compute paired differences d12 = v1-v2 and d13 = v1-v3 using fscalc (note that you do not need v2-v3). Next, create a new stack from d12 and d13 with mri_concat (eg, mri_concat d12.mgh d13.mgh --o d12+d13.mgh). Then create an FSGD file with a class for each group and two variables (d12 and d13)). The structure will look something like this: Input subject1 G1 1 0 Input subject2 G1 1 0 ... rest of subjects for group 1 ... Input subject1 G1 0 1 Input subject2 G1 0 1 ... rest of subjects for group 1 ... Input subject1 G2 1 0 Input subject2 G2 1 0 ... rest of subjects for group 2 ... Input subject1 G2 0 1 Input subject2 G2 0 1 ... rest of subjects for group 2 ... Run the analysis with DOSS. You can use the following contrast matrix to test for an interaction: [1 -1 -1 1] Let me know if that makes sense or not doug On 08/23/2012 09:39 PM, Shannon Kogachi wrote: Hi, Is there a way to set up a repeated measures ANOVA and ANCOVA with two different groups (ex: study group v. controls) and each subject has more than two timepoints? Would it be possible to assign each Input in the fsgd file to two classes (ex: timepoint scan and group) or is there another way to set up the fsgd file and contrast matrices? I've already used qdec in freesurfer 5.1 to calculate rates of change and symmetrized percent changes between the timepoints (using long_mris_slopes) but now would like to perform a repeated measures test. Thank you! -Shannon K. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer tutorial data
Instead of FTP, you could try getting the files via HTTP at http://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/ -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Tue, 4 Sep 2012 6:19pm, Dix Meiberth wrote: Thx for your responses. But no, I try to copy to my harddrive on my 1 year old Mac. I think for the fith time right now. There should be no limit but I will doublecheck. Best regards. Dix Von meinem iPhone gesendet Am 04.09.2012 um 20:56 schrieb Help Desk -- Paul Raines h...@nmr.mgh.harvard.edu: 2GB sounds like you reaching maybe a file size limit of your operating system if it is really old. Or if you have are trying to download to a FAT formated external USB drive or such. -- Paul Raines (http://help.nmr.mgh.harvard.edu) On Mon, 3 Sep 2012 11:32am, Bruce Fischl wrote: Hi Dix, not sure what's going on. Have you tried multiple times? Bruce On Mon, 3 Sep 2012, dix.meibe...@ukb.uni-bonn.de wrote: Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the bruckner_data_tutorial_subjs.tar.gz I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 dix.meibe...@ukb.uni-bonn.de 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] missing ROI when using mri_label2vol to transfer ic2.tri
Hi Longchuan, when I asked for the terminal output, I meant the stuff that gets printed to the screen when the command runs. Try running it outside of your script to capture the output. Also, does the old program require 20G ? doug On 08/27/2012 04:20 PM, Longchuan Li wrote: Hi, Doug Here is the output from my log file and my command. I have been running this command many times and sometimes the job got killed, but sometimes they finished without error. /usr/local/sge/bitc/spool/node13/job_scripts/77912: line 7: 30345 Killed /home/lli/freesurferv51/bin/mri_label2vol.linux --offset 1 --annot /home/lli/freesurferv51/subjects/RVJ8_Preuss_2015/label/rh.randomroi300_WithoutMedialWall.MacaqueYerkes6_to_RVJ8_Preuss_2015.annot --temp /home/lli/freesurferv51/subjects/RVJ8_Preuss_2015/mri/brain.mgz --subject RVJ8_Preuss_2015 --hemi rh --fillthresh 0 --proj frac 0 0.5 0.05 --o /home/lli/freesurferv51/subjects/RVJ8_Preuss_2015/mri/rh.randomroi300_WithoutMedialWall_Ribbon.MacaqueYerkes6_to_RVJ8_Preuss_2015_fill0_projs0_proje0.5_projin0.05.nii.gz --identity Many thanks in advance! Longchuan *From:* Douglas Greve gr...@nmr.mgh.harvard.edu *To:* Longchuan Li leonad...@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Monday, August 27, 2012 3:47 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri What is your command line and what is the terminal output? doug On 8/27/12 7:57 PM, Longchuan Li wrote: Hi, Doug This is a follow-up question regarding an updated code you sent to me earlier (mri_label2vol.linux). I noticed that this program frequently takes around ~20G RAM to run and easily get killed by Linux (I supposed) when I ran multiple subjects, because of the large amount of RAM used. Has anyone else proposed the issue? and if so, do you have any suggestions on solving the issue? Thank you! Longchuan *From:* Leon leonad...@yahoo.com mailto:leonad...@yahoo.com *To:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 3:48 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri Hi, Doug I have run and checked the data and the problem has been perfectly solved. Thank you for the help! Leon *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Leon leonad...@yahoo.com mailto:leonad...@yahoo.com *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, June 8, 2012 1:32 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri I've put a new version of mri_label2vol at that ftp site. When you run it, add --offset 1. This will change the segmentations IDs to go from 1-162 instead of 0-161. doug On 06/08/2012 11:30 AM, Leon wrote: Hi, Douglas I checked the data this morning and confirmed that the missing ROI in the volume space is vertex_0 (see attached). Totally there are 162 entries in the annotation file, but only 161 left in the volume file after transferring the annotation file to the volume using mri_label2vol and the intensity value ranges from 1 to 161. Thanks Leon PS: I am sending the message again because I was told that the image for the previous mail is too big. *From:* Leon leonad...@yahoo.com mailto:leonad...@yahoo.com *To:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *Cc:* FreeSurfer freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, June 7, 2012 10:52 PM *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri Hi, Douglas Thank you very much for taking care of it. The ROIs ending with 2 and 5s have been correctly labeled and have volumes now after running the fixed version of mris_make_face_parcellation. However, there is still one ROI missing in the volume data that is located at the top of the postcentral gyrus after the annotation file was transferred from the subject's surface to the volume using mri_label2vol. I checked the index of the ROI yesterday (I am at home now and do not have access to the data) and I remember the index of the missing ROI is vertex_0 and the location of the ROI is identical as the one in the picture I attached in the previous email. Do you think it might be because the mri_label2vol overlooks the index of 0, as the intensity value in the volumes starts with 1? I would appreciate your help on this. Leon *From:*
Re: [Freesurfer] Freesurfer-Error message
Thanks Bruce, Still no luck,this what I am getting /freesurfer/subjects/test1 recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/test7 mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FreeSurfer:~/freesurfer/subjects/test1 On 4 September 2012 14:37, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: if that's the name of the image file. Can you post the list on your replies so others can answer? thanks Bruce On Tue, 4 Sep 2012, Varghese Chikku wrote: Hi Bruce, Many thanks for you mail. Is this the command you referring to. recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image1.**dcm -subjid test4 Thanks Chikku On 3 September 2012 17:33, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Chikku you need to give it the path to an image file (any one will do) and it will figure out the other slices that makeup the same series. What is the resolution of your data? 50 slices isn't usually enough to cover the brain at high enough resolution to get good thickness results. cheers Bruce On Mon, 3 Sep 2012, Varghese Chikku wrote: Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /media/sf_freesurferstudys/** raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012 My image files, in dcm format, are at /media/sf_freesurferstudys/**raw/raw_scr/T1pre : /media/sf_freesurferstudys/**raw/raw_scr/T1pre ls Image1 Image00010 Image00019 Image00028 Image00037 Image00046 Image2 Image00011 Image00020 Image00029 Image00038 Image00047 Image3 Image00012 Image00021 Image00030 Image00039 Image00048 Image4 Image00013 Image00022 Image00031 Image00040 Image00049 Image5 Image00014 Image00023 Image00032 Image00041 Image00050 Image6 Image00015 Image00024 Image00033 Image00042 Image7 Image00016 Image00025 Image00034 Image00043 Image8 Image00017 Image00026 Image00035 Image00044 Image9 Image00018 Image00027 Image00036 Image00045 Many thanks for your help. chikku 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer-Error message
Is that the actual name of the file? Does it have a dcm extension? On Wed, 5 Sep 2012, Varghese, Chikku wrote: Thanks Bruce, Still no luck,this what I am getting /freesurfer/subjects/test1 recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/test7 mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FreeSurfer:~/freesurfer/subjects/test1 -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Dienstag, 4. September 2012 18:25 To: Varghese, Chikku Subject: Re: [Freesurfer] Freesurfer-Error message you need a -all at the end to tell it what to do. And please cc the list so others can answer! On Tue, 4 Sep 2012, Varghese, Chikku wrote: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test4 Is it this command I should use? The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FDR Correction of NHP Surface Data
Hi Clark, I just made a modification to mri_binarize to make it take an FDR as input. It computes the threshold and binarizes the input based on the threshold. I've put a copy here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux Run it with --help to get more info. doug On 08/29/2012 02:08 PM, Clark Fisher wrote: Hi Sebastian, I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model. At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well. I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: Hi Clark, On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: Hi Bruce, Thanks. I actually have used this function of tksurfer, but am looking for a way to save the corrected maps, so that they could be manipulated by other tools (for instance, viewed by PySurfer). Does it really correct the map? I thought all it does is figure out the corrected threshold. By the way, if I understand correctly, FDR maps should be considered to be binary, that is you really do not know which voxels might be false positives, so you should not interpret all voxels to be equally significant. Having said that, almost everybody I know still looks at the p-value spatial distribution when looking at those FDR thresholded maps… (then again, I do not know any statistician...) best Sebastian I recognize that this may not be an officially supported functionality, but is there some way to save the adjusted overlays from tksurfer, or create them in some other way? Best, Clark On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: Hi Clark you shouldn't need either. Load your overlays then click the button to compute the FDR threshold in the tksurfer configure overlay interface. cheers Bruce On Tue, 28 Aug 2012, Clark Fisher wrote: Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark ___ 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 -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moel...@caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] mri_watershed and other errors.
Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren attachment: FS_error.jpg___ 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] resending question about 3rd level analysis
Hi Susan, I've updated that web page to demonstrate how to run the random effects analysis. Let me know if that is clear or not. doug On 08/23/2012 12:38 PM, Susan Alice McLaughlin wrote: Hi, I'm resending this e-mail, as it didn't seem to go through correctly yesterday: I’m a Freesurfer novice, and I’m confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis in FSL. Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc. I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using: mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label However, I want to use a random as opposed to fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysis, do I need to correct for multiple comparisons? Many thanks in advance, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] mris_anatomical_stats on multiple subjects
Hi again, This is a follow-up question to my previous email -- the method I used may not be the most efficient or the correct way to extract cortical thickness from manually created ROIs. I'm unfamiliar with how to obtain thickness data from a label, so I'm not sure if what I did is correct or if first I must convert my label to volume or to an annotation file. If anyone knows a better or more accurate way to measure thickness from the ROI I'd really appreciate your advice! Best, Alex Hi Doug and Freesurfers, I'm currently working on extracting thickness measurements from an ROI I manually created. I created my ROI label in tksurfer and applied the label to each subject I'd like to extract thickness data from using mri_label2label. I then used the following command to generate a stats file, with the thickness measurement, from my label: mris_anatomical_stats -f something.stats -l something.label subjid ?h (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit). This generated a stats file that gave me the average thickness for my ROI in my subject. I was wondering if there is a way to run the same command, but on multiple subjects at once, so as not to have to run this command on each individual subject. Any suggestions would be greatly appreciated! Best, Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_watershed and other errors.
Hi Darren can you describe your input data? What format, resolution, etc... is it? If you upload it we'll take a look cheers Bruce On Wed, 5 Sep 2012, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ 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_watershed and other errors.
Bruce: Thank you for looking. I have uploaded the files: I uploaded them in Dicom Format. This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1. Name: 3157.tar.gz Darren On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Darren can you describe your input data? What format, resolution, etc... is it? If you upload it we'll take a look cheers Bruce On Wed, 5 Sep 2012, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren 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. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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] Repost: Converting BV ROIs to FS
Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly? Thanks for all your help! Katie On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point xtal ytal ztal cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie 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. ___ 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] creating a gca file from .mgz files
I don't think you actually want to do the full conformation as that will change the type to uchar, which is probably what is messing up your values. Instead, try this mri_vol2vol --mov aseg.mgz --targ orig.mgz --regheader --interp nearest --precision int --o aseg.conf.mgz doug On 09/05/2012 12:47 PM, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz
Re: [Freesurfer] creating a gca file from .mgz files
what is your mri_convert command line? On Wed, 5 Sep 2012, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
Re: [Freesurfer] Covary for categorical variable in QDEC
Hi Jeff, sorry, what do you mean to covary for a categorical variable? doug On 09/05/2012 12:43 AM, Jeff Sadino wrote: Hello, Is it possible to covary for a categorical variable in QDEC? I see other posters have said it is not possible, but I did not see any official documentation or response regarding the issue. Thank You, Jeff Sadino ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Repost: Converting BV ROIs to FS
Nevermind, it turns out it was due to an permissions error. Thanks again. Katie On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt k...@wjh.harvard.eduwrote: Ok, I am trying to use the select_talairach_point command, and I have it in part of a script that uses tksurfer to load up a subject's inflated surface, load the curvature, and load an overlay, but it doesn't seem to be doing anything. Is there a step I am missing? What should I see if it works correctly? Thanks for all your help! Katie On Wed, Sep 5, 2012 at 9:19 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Katie you can view data on a tal brain by mapping the data using the talairach.xfm transform. Since you can also use the inverse of the transform you can map both ways. I think there is a tcl command in tksurfer for finding the vertex that is closest to a given tal coord. Try: select_talairach_point xtal ytal ztal cheers Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: Hrm. Ok, is there any way to view data for a subject in Freesurfer on a talairach transformed brain? What I would be hoping to do is bring up the data in native subject space, make any ROI label, then also bring the data up on a talairach transformed brain, make a ROI label, then put both labels on the same brain (either native or talairach transformed) and see if they are any different. Also, is there a way to input a particular talairach vertex and jump to that in freesurfer, instead of just moving the mouse around and hoping to find the right spot? Katie On Tue, Sep 4, 2012 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I don't think anyone here knows how to do this as we don't use it. Perhaps the Brain Voyager people do? sorry, Bruce On Tue, 4 Sep 2012, Katie Bettencourt wrote: So our lab is running a couple analyses and we are getting different results based on whether we use Brain Voyager or Freesurfer that we think is due to different ROI selection across the two platforms. Is there anyway to load a BrainVoyager ROI into freesurfer? The BV data has been talairach transformed, does that matter? Less optimal would be loading a freesurfer ROI into BV, but if that's easier, we could try that way too. Any help would be appreciated. Katie 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. ___ 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_watershed and other errors.
Darren, I forgot to mention that you'll need to add -clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ 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] tksurfer not working properly
Deirdre, this is the infamous 'sliver' problem. consult this page for solutions: https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Nick On Wed, 2012-09-05 at 13:39 -0400, Deirdre O Shea wrote: Hello, I am just getting to get grips with using FreeSurfer to reconstruct images, however, any time I try to load tksurfer it only displays a very small part of the image (see attached for what i mean). I was hoping someone could give me an explanation as to why this may be happening and whether there is a solution to fixing it. Best Deirdre ___ 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] Covary for a categorical variable in mri_glmfit
Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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] Covary for a categorical variable in mri_glmfit
I still don't know what you mean by covarying for gender. What is your design? Can you send your FSGD file? doug On 09/05/2012 04:44 PM, Jeff Sadino wrote: Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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_watershed and other errors.
I'm running it now with the current dev version and it's passed the skull stripping stage and it seems to have worked fine... On Wed, 5 Sep 2012, Nick Schmansky wrote: Darren, I forgot to mention that you'll need to add -clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_watershed and other errors.
Bruce I used the following version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 Is that the same as the one you are using or are you referring to an internal development version? I will try Nick's suggestion as well. Darren On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: I'm running it now with the current dev version and it's passed the skull stripping stage and it seems to have worked fine... On Wed, 5 Sep 2012, Nick Schmansky wrote: Darren, I forgot to mention that you'll need to add -clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ 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. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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_watershed and other errors.
Nick I ran: recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157 and got the exact same problem with brainmask.mgz Darren On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Darren, I forgot to mention that you'll need to add -clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ 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. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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_watershed and other errors.
our internal development version. On Wed, 5 Sep 2012, Darren Gitelman wrote: Bruce I used the following version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 Is that the same as the one you are using or are you referring to an internal development version? I will try Nick's suggestion as well. Darren On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I'm running it now with the current dev version and it's passed the skull stripping stage and it seems to have worked fine... On Wed, 5 Sep 2012, Nick Schmansky wrote: Darren, I forgot to mention that you'll need to add -clean-bm after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be retained and the new one will be saved as brainmask.auto.mgz. Nick On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote: Nick, List: Still no luck with this data. See attached as an example. To get to this point I had run: recon-all -all This ran to the error: mri_watershed Error: GLOBAL region of the brain empty ! Then I followed your recommendation below recon-all -s subjid -skullstrip -no-wsgcaatlas, which had no errors and then recon-all -s subjid -autorecon2 -autorecon3 This produced the result attached. I then deleted this directory and re-imported all the dicom data for this subject. Looked at the images, which look fine. Then I ran recon-all -s subjid -autorecon1 This fails with the mri_watershed error. Then I ran recon-all -s subjid -skullstrip -no-wsgcaatlas. This runs without error but when I look at the brainmask.mgz it looks just like the attached image. Is there some way to set the thresholds differently? The T1 image looks fine to me although perhaps the intensity is slightly less than usual, but it doesn't seem particularly noisy. Darren ___ 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. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ 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] Covary for a categorical variable in mri_glmfit
Hello, I think our emails were getting crossed in cyberspace. I have a group that has a disproportionate number of females, and so there is a significant difference in the number of females as compared to males (chi-square p=.01). This must be accounted for. If I find that one group has a smaller brain volume, etc., then it could be attributed to one group having fewer females than the others. My ultimate goal is to run an analysis on the thickness, taking into account these sex differences (and ICV and age). My plan was to covary for sex, icv, and age. I have covaried for icv and age lots of times, but I am having trouble covarying (if that is the right word) for this categorical sex variable. Any help would be greatly appreciated! Jeff On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino jsadino.que...@gmail.comwrote: Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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] Covary for a categorical variable in mri_glmfit
Use gender as a discrete variable in the FSGD, ie, a class for M and a class for F. If you have two other groups (say, normals and patients), then use four classes (Mnormals, Mpatients, etc). Then test for the normals vs patients with (Mnorm+Fnorm) - (Mpat+Fpat). This regresses out gender. doug On 9/5/12 8:10 PM, Jeff Sadino wrote: Hello, I think our emails were getting crossed in cyberspace. I have a group that has a disproportionate number of females, and so there is a significant difference in the number of females as compared to males (chi-square p=.01). This must be accounted for. If I find that one group has a smaller brain volume, etc., then it could be attributed to one group having fewer females than the others. My ultimate goal is to run an analysis on the thickness, taking into account these sex differences (and ICV and age). My plan was to covary for sex, icv, and age. I have covaried for icv and age lots of times, but I am having trouble covarying (if that is the right word) for this categorical sex variable. Any help would be greatly appreciated! Jeff On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino jsadino.que...@gmail.com mailto:jsadino.que...@gmail.com wrote: Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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.
