Re: [Freesurfer] Hippocampus Doubt
Thanks BruceYes and no, we did sum all the outputs from the subfields segmentation, but I didnot find the fornix, Is it included I. The fimbria? What would be the difference if I do not include this label? And what do you mean with different definitions of what's and is not included?Regards,GabrielEl 12/07/12, Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:Hi Gabriel,certainly they won't match as (a) they are different algorithms, and (b) they are different definitions of what is and is not included. Did you sum up things like fimbria and fornix in your subfield totals?cheersBruceOn Thu, 12 Jul 2012, Gabriel Gonzalez Escamilla wrote:Hello,after applying hippocampal subfield segmentation to our sample, we noted that summation of hippocampal subfields (in mm3) differs considerably from hippocampal volume (derived from aseg) in some of our subjects:case 1: 2592 mm3 (aseg hipp. volume) versus 2116 mm3 (summation of hipp. subfields)case 2: 4764 mm3 (aseg hipp. volume) versus 4002 mm3 (summation of hipp. subfields)case 3: 1914 mm3 (aseg hipp. volume) versus 2110 mm3 (summation of hipp. subfields)Please let me know why this is happening, and if this mismatching can be considered normal.Thank you very much in advance.Best regards,GabrielThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] Using SPM transformation matrices as initial guess in talairach_avi
Hi Avi and Bruce, thanks for your replies. Indeed we use the inverse of the T1 values i.e. 'R1' maps (units in 1/ms although I scaled WM to 110; colloquially we use T1/R1 interchangebly, sorry). The contrast is comparable to freesurfer output T1.mgz and of course different from the larger flip angle FLASH. I will follow your both suggestions, i.e. try to process the FLASH and also the pre-realinged R1 maps in case freesurfer registration step fails. Cheers Simon Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 12. Juli 2012 22:16 Bis: Snyder, Avi Cc: Baudrexel, Simon; freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: AW: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi Hi Simon I'm also puzzled about your quantitative T1 maps. Are these T1 values in ms? If so, the image won't have T1-weighted contrast as WM will be darker (shorter T1) than GM, in which case everything would fail. I assume that what you are going to FreeSurfer (and Avi's code) is instead the larger flip angle FLASH image. cheers Bruce On Thu, 12 Jul 2012, Snyder, Avi wrote: I don't see that it is possible to avoid double resampling if you use FreeSurfer to segment. As far as I can tell, the problem with your dataset is that a substantial fraction of cases results a clearly poor Talarrach atlas transform, e.g., too fat or too thin or distorted. There is no provision, as far as I am aware, to, initialize the Talairach transform module based on a prior computations. There are two main possibilities that underly bad Talairach transforms (1) input images very displaced or rotated from standard acquisitions (2) mismatch between contrast mechanisms in the sample T1W and the atlas representative target. It is possible to correct error mechanism 2. A dialog regarding this possibility is ongoing with the FreeSurfer developers. Avi --- On 7/12/12 5:09 AM, Baudrexel, Simon simon.baudre...@kgu.de wrote: Dear Avi, thank you for your reply, probably I didn't make my point clear enough. Our high resolution quantitative T1-maps (derived from multispectral FLASH) have excellent GM-WM contrast and once autorecon1 (talairach-avi) gets over this tricky coregistration into standard space all other following steps look very fine (including the subcortical segmentation which I'm interested in). Since registration is often more robust when images are approximately realigned from the beginning, I thought to use SPM (or fsl) affine coregistration parameters (to MNI space) as a guess in talairach_avi would be worth a try (I think the problem lies in a somewhat different contrast of the neck and skull which appear brighter in our qT1 maps compared to MPRAGE). I could use SPM-coregistered T1 maps instead an put them into the freesurfer pipeline which, however, would mean an additional interpolation (which is not what I want). Is there another workaround? ( I read that in tkregister2 there is the option to apply fsl transformation matrices - something like that would be needed - but I'm no too familiar with the way freesurfer handels and stores those transformations). As my doctorate fellow sees himself manually segmenting all the subcortical structurs any help would be greatly appreciated -:) Thanks, Simon Baudrexel Brain Imaging Center Goethe University Frankfurt Von: Snyder, Avi [a...@npg.wustl.edu] Gesendet: Donnerstag, 12. Juli 2012 01:58 Bis: Baudrexel, Simon; Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi Simon, The standard Talairach atlas transform module in FreeSurfer was designed for T1W high-resolution structural images (e.g., MP-RAGE or SPGR). This is a design choice partly driven by the fact that the FreeSurfer segmentation algorithm assumes high-resolution T1 weighting. Reliable atlas transformation with any other contrast mechanism would be highly uncertain. Atlas transformation modules theoretically could be produced for other contrast mechanisms, e.g., R1 or FA. However, it is not clear that, even if this were done, that the tissue classification part of FreeSurfer would work. If you have R1 and/or FA images that need to be analyzed using FreeSurfer segmentations, I would think that you should submit a minimally processed high-resolution T1W image to FreeSurfer and then use the generated results as ROIs in subsequent analyses. Of course, this strategy requires that the images containing the contrast to be evaluated are co-registered to the segmented MP-RAGE. I hope I have correctly understood your scientific objectives. Avi Snyder On 7/10/12 4:20 AM, Baudrexel, Simon simon.baudre...@kgu.de wrote: Hi Bruce, I'm using freesurfer version 5.1.0. I currently try to process quantitative T1 (R1)
Re: [Freesurfer] error message for recon-all
Thank you so much Bruce, it now works like a charm! Best, Muriel On Jul 12, 2012, at 2:30 AM, Bruce Fischl wrote: Hi Muriel not sure what your second frame is, but you should be able to do this: cd $SUBJECTS_DIR/subject id/mri/orig mv 001.mgz multiframe.mgz mri_convert -nth 0 multiframe.mgz 001.mgz recon-all -s subject id -all cheers Bruce On Thu, 12 Jul 2012, Muriel Bruchhage wrote: Maybe this is easiest: Best, Muriel On Jul 12, 2012, at 12:54 AM, Bruce Fischl wrote: did it have 2 frames? If so, what is the difference between them? On Thu, 12 Jul 2012, Muriel Bruchhage wrote: Hi Bruce, I tried to send the .mgz file to you, but it apparently exceeded the limit. Nevertheless, I thought that it looked fine (I compared it to the bert data freesurfer came with). Thank you very much again for all your efforts! Best, Muriel On Jul 11, 2012, at 11:51 PM, Bruce Fischl wrote: you can run freeview on the 001.mgz and see what is in it. If it has more than one frame freeview will include a slider that lets you change from one to the other. Or you can email it to me and I'll take a look. On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hi Bruce, To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there. Best, Muriel On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: Hi Muriel what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: I added the -all at the end and skipped the -i flag, but I still get an error message: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz has 2 frames I am so sorry to bother you with these probably very amateur questions - but how can I have multiple frames when I just got one .mgz file and just one T1? Best, Muriel On Jul 11, 2012, at 10:55 PM, Bruce Fischl wrote: oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i path to dicom cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folders are - could that have been the problem? (this is also the same place where my $SUBJECTS_DIR is directed to) Best, Muriel On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: Hi Bruce, Thank you very much for your fast response. Unfortunately though, I still get an error response when typing in recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 recon-all -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -subjid GID02 Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM Actual FREESURFER_HOME /Applications/freesurfer Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz corRead(): can't open file /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64 recon-all -s GID02 exited with ERRORS at Wed Jul 11 18:32:26 CEST 2012 For more details, see the log file
[Freesurfer] mapping label to vol and aseg to vol
Hi FreeSurfer team, I have two small questions related to exporting label or aseg into mgz volumes: 1) I want to save one label into a volume, I used mri_label2vol which works perfectly, but I am getting only a thin label. I saw that I can use the --proj option with mri_label2vol to increase the thickness of my label, but I was wondering if there is any way to obtain the whole cortical ribbon corresponding to the label (i.e. something looking like the volumetric counterpart of the parcellation as found in the aparc+aseg.mgz)? 2) Similarly, I wanted to export the 5 subregions of the corpus callosum as individual volumes (i.e. one mgz volume for each subregions). Is that any way to do that? Or to export the 5 CC subregions as labels that could be then loaded on the cortical surface? Many thanks for your help, Marie ___ 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] mapping label to vol and aseg to vol
Hi Marie for 2 you can do either mri_binarize --match or mri_extract_label. For 1 you can put your label into a .annot, then use mri_aparc2aseg (which is what we use to create the aparc+aseg.mgz). cheers Bruce On Fri, 13 Jul 2012, Marie Schaer wrote: Hi FreeSurfer team, I have two small questions related to exporting label or aseg into mgz volumes: 1) I want to save one label into a volume, I used mri_label2vol which works perfectly, but I am getting only a thin label. I saw that I can use the --proj option with mri_label2vol to increase the thickness of my label, but I was wondering if there is any way to obtain the whole cortical ribbon corresponding to the label (i.e. something looking like the volumetric counterpart of the parcellation as found in the aparc+aseg.mgz)? 2) Similarly, I wanted to export the 5 subregions of the corpus callosum as individual volumes (i.e. one mgz volume for each subregions). Is that any way to do that? Or to export the 5 CC subregions as labels that could be then loaded on the cortical surface? Many thanks for your help, Marie ___ 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] Cutting non-cortex
Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets? I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools. Thanks, Sourena Soheili ___ 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.
