Re: [Freesurfer] Question about the outputs of recon-all
Hi, Douglas Thanks for your reply. So, as you stated, the fsaverage is already in the MNI space? Because my fMRI data are in the MNI space (after normalization) and I want to extract the region with significant different cortical thickness as seed to calculate functional connectivity. Best, Feng 发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu 发送时间：2015-08-12 22:39 主题：Re: [Freesurfer] Question about the outputs of recon-all 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： fsaverage is the surface-based common-space analogous to talairach for MNI space. This is the space where group analysis is done on the surface. You can run mris_preproc to get a stack of data in fsaverage space prior to running group analysis with mri_glmfit. See the on-line tutorials on the wiki. On 08/11/2015 09:46 PM, chenhf_uestc wrote: Dear Freesurfer experts, I am a new user of freesurfer and I just performed recon-all analyses. I have some questions about the pipeline (may be very simple ^_^). In the fMRI, I used SPM8 toolkit to perform preprocessing. After normalization, the images were transform to the MNI space. In the freesurfer, there are many folders in the output subject dir, e.g., bem, mri, script, surf. The first question, were the recon-all analyses performed in the individual spave (I mean, unlike spm or other software, there is no normalization procedure in freesurfer)? If in the individual space, we should transform all subjects' files into a common space for group-level analysis. How can I transform them? Did I transfrom these into MNI space or other space? In the fswiki, I have known that there is a fsaverage space. So, the second question is that what is the fsaverage space and what is the aim to introduce such space. Can I regard fsaverage space as a intermediate between individual space and MNI space? Further, in the recon-all analysis, there is a procedure of talairach transformation. Were the outputs transformed into talairach space? Any help will be greatly appreciately! Best, Feng ___ 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] mris_preproc -iv option
Dear Freesurfer team, How does mris_preproc map volume data onto the surface when using the -iv option? Is an average between the white and pial boundaries taken, or are only the voxels taken into account that intersect with one of the two surfaces (and if yes, with which surface)? mris_preproc--iv volmeasfileSpecify full path to a volume file and its registration matrix file. The registration matrix file is of the type accepted/created by tkregister2. The volume is sampled to the surface, and the result is used as the input surface measure. This is an alternative to using --meas. This still requires that a subject list be supplied. Thanks again! Best, Silas ___ 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 my questions: Issues with first attempt in viewing Tracula output
Dear Anastasia, I send (uploaded) the files on Monday. Could you please confirm that they arrived. Thank you so very much for looking into it. Leora. Leora Amira, PhD Columbia University NYS Psychiatric Institute Division of Child and Adolescent Psychiatry 1051 Riverside Drive New York, NY 10032 amir...@nyspi.columbia.edu Office: 646-774-5820 On 8/7/15, 6:17 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu wrote: Hi Leora - I regret to inform you that it's the processing that has failed, pretty much for all the tracts. I'm guessing it's an earlier preprocessing (likely registration) step that has failed. If you upload the tracula output directories (dmri, dlabel, dpath) of your subject for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Please also send your trac-all.log. Thanks! a.y On Fri, 24 Jul 2015, Leora Amira wrote: Thank you very much. From: Leora Amira amir...@nyspi.columbia.edu Date: Thursday, July 23, 2015 at 2:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Issues with first attempt in viewing Tracula output Hi, This is my first time using Tracula. I processed a large number of subjects¹ DTI scans and am now viewing the results in Freeview (I copied the commands from Tracula wiki tutorial). The images look somewhat peculiar in several ways. I am attaching screenshots with a few questions. 1. All my images look jaggedy and not smooth and beautiful like in the Tracula wiki tutorialŠ. (image 1: ilf)[IMAGE] 2. Tracts are truncated: Corpus callosum forceps are not complete (image 2)[IMAGE] 3. Tracts are displaced: Corpus callosum forceps are displaced and out of the brain template (image 3)[IMAGE] 4. All tracts seem truncated and not exactly in the right place (image 4[IMAGE] Are the errors in the viewing or, I so hope not, in the processing? And if so, what might be the errors and how to correct them? Thank you very much. Grateful. ___ 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] pial-outer-smoothed misalignment
Would it be possible to send me the surface and the volume that do not align in freeview? Thanks, Ruopeng On 08/13/2015 11:46 AM, Roan LaPlante wrote: Hello, I am trying to use mris_compute_lgi to create the smoothed pial surface with no gyri, and then use this surface for a different purpose than the LGI. To do this I simply modified a version of the mris_compute_lgi script to run up until the creation of the *h.pial-outer-smoothed surfaces. When examining the surface in tkmedit it appears to align with the pial surface correctly. But I tried to open the surfaces in freeview and saw that the surface coordinates do not match the volume. At a glance the misalignment may only be a translation in the A/P direction. Is there a reason why the coordinates in this surface differ from the subject RAS space and what transformation is tkmedit applying to align them? thanks, -- Roan LaPlante Athinoula A. Martinos Center for Biomedical Imaging ___ 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] Loading .w surface overlay in Freeview
Dear all, I am wondering if there is a facility for loading .w overlay files in Freeview? In the surface section of the GUI, the overlay tab is for volumetric files (.mgz, .nii, etc.). In the command line, the overlay option fails - for example: freeview -f /path/to/lh.inflated:overlay=/path/to/overlay.w returns this error message in the GUI: Failed to load surface overlay. mri_read() and this one in the command line: : couldn't determine type of file /path/to/overlay.w The .w file in question was produced with mri_vol2surf. Any suggestions? -- Kind regards, Ivan Alvarez PhD Candidate Imaging and Biophysics Unit UCL Institute of Child Health 30 Guilford Street, London, WC1N 1EH ___ 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] cannot find qdec file
do you mean the one without the blank line at the end? I've attached that for you. Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 13. August 2015 18:12:40 Betreff: Re: [Freesurfer] cannot find qdec file Can you send the new qdec table file? On 08/05/2015 04:05 AM, Clara Kühn wrote: no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 4. August 2015 20:43:47 Betreff: Re: [Freesurfer] cannot find qdec file oops, sorry for the delay, thanks for the reminder. The problem is that you have a blank line at the end of your long.qdec.table.dat file. Remove the line and see if it works. doug On 08/04/2015 12:42 PM, Clara Kühn wrote: Hi Doug, did the fordoug.log file give any information about why FreeSurfer can't find my qdec file? Cheers and thanks for working on this! Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 17:16:18 Betreff: Re: [Freesurfer] cannot find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. and the actual qdec file is attached. Cheers, Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 Betreff: Re: [Freesurfer] cannot find qdec file Can you send your command line, full terminal output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 Betreff: Re: [Freesurfer] cannot find qdec file that is probably not the full path. Try typing ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat If it says it cannot find the file, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 Betreff: Re: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh It always says ERROR: cannot find qdec/long.qdec.table.dat Yes, the walkthrough asks for an input file named just qdec.table.dat, but I haven't got that. So far in the longitudinal stream there are long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat files. So I figured I'd use the long.qdec file because FS needs to get the information about the long timepoints. But it cannot find the file, even though I see it. I've also tried copying the long.qdec file and naming it qdec.table.dat but it still doesn't find it. The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and my SUBJECTS_DIR is scr/etsch2/kids/ct Can you help me see what I'm missing? Thanks a lot in advance, Clara ___ 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
Re: [Freesurfer] Resending my questions: Issues with first attempt in viewing Tracula output
I am glad I checked. Yes, I did use your email. I will tray to upload it again into the link you sent and I will email you to let you know when I had done that. Leora Amira, PhD Columbia University NYS Psychiatric Institute Division of Child and Adolescent Psychiatry 1051 Riverside Drive New York, NY 10032 amir...@nyspi.columbia.edu Office: 646-774-5820 On 8/13/15, 11:41 AM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu wrote: Sorry, didn't get anything! Did you use me as the recipient (ayendiki)? On Thu, 13 Aug 2015, Leora Amira wrote: Dear Anastasia, I send (uploaded) the files on Monday. Could you please confirm that they arrived. Thank you so very much for looking into it. Leora. Leora Amira, PhD Columbia University NYS Psychiatric Institute Division of Child and Adolescent Psychiatry 1051 Riverside Drive New York, NY 10032 amir...@nyspi.columbia.edu Office: 646-774-5820 On 8/7/15, 6:17 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu wrote: Hi Leora - I regret to inform you that it's the processing that has failed, pretty much for all the tracts. I'm guessing it's an earlier preprocessing (likely registration) step that has failed. If you upload the tracula output directories (dmri, dlabel, dpath) of your subject for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Please also send your trac-all.log. Thanks! a.y On Fri, 24 Jul 2015, Leora Amira wrote: Thank you very much. From: Leora Amira amir...@nyspi.columbia.edu Date: Thursday, July 23, 2015 at 2:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Issues with first attempt in viewing Tracula output Hi, This is my first time using Tracula. I processed a large number of subjects¹ DTI scans and am now viewing the results in Freeview (I copied the commands from Tracula wiki tutorial). The images look somewhat peculiar in several ways. I am attaching screenshots with a few questions. 1. All my images look jaggedy and not smooth and beautiful like in the Tracula wiki tutorialŠ. (image 1: ilf)[IMAGE] 2. Tracts are truncated: Corpus callosum forceps are not complete (image 2)[IMAGE] 3. Tracts are displaced: Corpus callosum forceps are displaced and out of the brain template (image 3)[IMAGE] 4. All tracts seem truncated and not exactly in the right place (image 4[IMAGE] Are the errors in the viewing or, I so hope not, in the processing? And if so, what might be the errors and how to correct them? Thank you very much. Grateful. ___ 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] Caret Human_Macaque.PALS_B12 to freesurfer
Dear ladies and possibly gentlemen as well, I have got a rather nasty question. I would like to import the following caret file Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape into free surfer and bring it into fs average space. In a next step I would like to import the caret/fsaverage result into matlab and do some stuff with it. There seems to be a mismatch between caret and freesurfer in the vertex numbers. Has somebody every tried this? Can it be done? I am not familiar with caret and would like to avoid using it. Alternatively there is matlab toolbox for caret. But I have no clue how to get from one ico vertex system into another. Greetings Jan Jan Willem Koten (van Grevenbicht) Neurological Clinic at the RWTH Aachen Pauwelstrae 30, 52074 Aachen, Germany Telephone: (0049) (0)241 8089909 ___ 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] Caret Human_Macaque.PALS_B12 to freesurfer
Hi Jan have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike Harms or Matt Glasser can chime in? Bruce On Thu, 13 Aug 2015, Jan Willem Koten wrote: Dear ladies and possibly gentlemen as well, I have got a rather nasty question. I would like to import the following caret file „Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape“ into free surfer and bring it into fs average space. In a next step I would like to import the caret/fsaverage result into matlab and do some stuff with it. There seems to be a mismatch between caret and freesurfer in the vertex numbers. Has somebody every tried this? Can it be done? I am not familiar with caret and would like to avoid using it. Alternatively there is matlab toolbox for caret. But I have no clue how to get from one ico vertex system into another. Greetings Jan Jan Willem Koten (van Grevenbicht) Neurological Clinic at the RWTH Aachen Pauwelstraße 30, 52074 Aachen, Germany Telephone: (0049) (0)241 8089909 ___ 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] Exporting the Hippocampus
Hi Chester the voxel coords reflect positioning in the scanner and so there is a lot of variability in them depending on landmarking, head size, etc... cheers Bruce On Thu, 13 Aug 2015, Chester Dolph wrote: I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the z (axial) axis. Of note, the hippocampus center of mass seem to fluctuate over a wider range of values than I was expecting- one hippocampus might exist in the 85 to 108 axial slices, while another hippocampus might exist in the 120 to 142 slices. I am intending to perform voxelwise analysis over a dataset. Is there an additional step/flag that aligns MRI in terms of the axial dimension? I used the recon all with the hippocampus flags. On May 8, 2015, at 3:21 PM, Chester Dolph cdolp...@odu.edu wrote: Thanks! On May 8, 2015, at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_binarize with the match option to get a mask of hippocampus from aseg.mgz (use 17 or left hippo and 53 for right, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then use mri_mask to mask the norm.mgz to get a volume of the intensities doug On 05/08/2015 03:11 PM, Chester Dolph wrote: In the last post I meant “using: Would the correct way of extracting the intensities using the segmentation look something like this? I would like to use raw intensity values of a ROI for texture analysis. I would prefer to have all of the extracted ROI in the same coordinate space so comparisons may be made between MRI scans. By “extract”, I mean isolate the ROI and ignore all other volumes. On May 8, 2015, at 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you say extract what do you mean exactly? On 05/08/2015 02:36 PM, Chester Dolph wrote: So I looked up the aseg file and the taliarch.label_intensities.txt. Would the correct way of extracting the intensities from the segmentation look something like this? if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., Right_hippocampus values 1.49 0.0 94) my extracted mri voxel = brain.mgz voxel else my extracted mri voxel = 0 end (if there’s a nice script or command that does this, please let me know). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ 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
Re: [Freesurfer] Loading .w surface overlay in Freeview
can you use vol2surf to generate a .mgz/.mgh file instead? We have deprecated the use of .w files On Thu, 13 Aug 2015, Ivan Alvarez wrote: Dear all, I am wondering if there is a facility for loading .w overlay files in Freeview? In the surface section of the GUI, the overlay tab is for volumetric files (.mgz, .nii, etc.). In the command line, the overlay option fails - for example: freeview -f /path/to/lh.inflated:overlay=/path/to/overlay.w returns this error message in the GUI: Failed to load surface overlay. mri_read() and this one in the command line: : couldn't determine type of file /path/to/overlay.w The .w file in question was produced with mri_vol2surf. Any suggestions? ___ 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] Exporting the Hippocampus
Hi Bruce, Thanks for the response. For ROI such as the hippocampus, is there a standard/accepted technique for voxelwise analysis? For instance, taking the meatiest slice of each subject (the slice with most nonzero voxels) and using that as the center slice. Then perform voxel base analysis on all of the subjects center slices (with additional ± 5 slices from the center slice). I am planning to use SVM using the voxels and compare with neural networks. Thanks, Chester PS if anyone has a favorite journal article on this concept, please share. On Aug 13, 2015, at 1:11 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Chester the voxel coords reflect positioning in the scanner and so there is a lot of variability in them depending on landmarking, head size, etc... cheers Bruce On Thu, 13 Aug 2015, Chester Dolph wrote: I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the z (axial) axis. Of note, the hippocampus center of mass seem to fluctuate over a wider range of values than I was expecting- one hippocampus might exist in the 85 to 108 axial slices, while another hippocampus might exist in the 120 to 142 slices. I am intending to perform voxelwise analysis over a dataset. Is there an additional step/flag that aligns MRI in terms of the axial dimension? I used the recon all with the hippocampus flags. On May 8, 2015, at 3:21 PM, Chester Dolph cdolp...@odu.edu wrote: Thanks! On May 8, 2015, at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_binarize with the match option to get a mask of hippocampus from aseg.mgz (use 17 or left hippo and 53 for right, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then use mri_mask to mask the norm.mgz to get a volume of the intensities doug On 05/08/2015 03:11 PM, Chester Dolph wrote: In the last post I meant “using: Would the correct way of extracting the intensities using the segmentation look something like this? I would like to use raw intensity values of a ROI for texture analysis. I would prefer to have all of the extracted ROI in the same coordinate space so comparisons may be made between MRI scans. By “extract”, I mean isolate the ROI and ignore all other volumes. On May 8, 2015, at 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you say extract what do you mean exactly? On 05/08/2015 02:36 PM, Chester Dolph wrote: So I looked up the aseg file and the taliarch.label_intensities.txt. Would the correct way of extracting the intensities from the segmentation look something like this? if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., Right_hippocampus values 1.49 0.0 94) my extracted mri voxel = brain.mgz voxel else my extracted mri voxel = 0 end (if there’s a nice script or command that does this, please let me know). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ 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
Re: [Freesurfer] Exporting the Hippocampus
I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the z (axial) axis. Of note, the hippocampus center of mass seem to fluctuate over a wider range of values than I was expecting- one hippocampus might exist in the 85 to 108 axial slices, while another hippocampus might exist in the 120 to 142 slices. I am intending to perform voxelwise analysis over a dataset. Is there an additional step/flag that aligns MRI in terms of the axial dimension? I used the recon all with the hippocampus flags. On May 8, 2015, at 3:21 PM, Chester Dolph cdolp...@odu.edu wrote: Thanks! On May 8, 2015, at 3:15 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_binarize with the match option to get a mask of hippocampus from aseg.mgz (use 17 or left hippo and 53 for right, see $FREESURFER_HOME/FreeSurferColorLUT.txt). Then use mri_mask to mask the norm.mgz to get a volume of the intensities doug On 05/08/2015 03:11 PM, Chester Dolph wrote: In the last post I meant “using: Would the correct way of extracting the intensities using the segmentation look something like this? I would like to use raw intensity values of a ROI for texture analysis. I would prefer to have all of the extracted ROI in the same coordinate space so comparisons may be made between MRI scans. By “extract”, I mean isolate the ROI and ignore all other volumes. On May 8, 2015, at 2:54 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: when you say extract what do you mean exactly? On 05/08/2015 02:36 PM, Chester Dolph wrote: So I looked up the aseg file and the taliarch.label_intensities.txt. Would the correct way of extracting the intensities from the segmentation look something like this? if( aseg.mgz voxel == my taliarch label intensity of interest (e.g., Right_hippocampus values 1.49 0.0 94) my extracted mri voxel = brain.mgz voxel else my extracted mri voxel = 0 end (if there’s a nice script or command that does this, please let me know). Thanks, Chester On May 8, 2015, at 1:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: do you mean the hippocampus in aseg.mgz or the hippocampal subfields? On 05/08/2015 01:26 PM, Chester Dolph wrote: Hello, Rewording to clarify in case the wording was confusing. What is the best way to use the segmented hippocampus outputs as a masks on the registered MRI to extract the hippocampus intensities? I would like to use FreeSurfer to extract the hippocampus and then perform analysis on the raw intensities (meaning the processed, ‘recon-all’ MRI ). I noticed that the segmented hippocampus outputs have different dimensisons that the brain.mgz files and thus I am unsure how align the hippocampus outputs for using them as masks. Thanks, Chester On Apr 29, 2015, at 2:17 PM, Chester Dolph cdolp...@odu.edu wrote: Hi, I would like to export the processed *.mgz of the Freesurfer pipeline and segmentation of hippocampal subfields *.mgz to *.nii files. I would like to later use the segmentation of the hippocampal subfields as masks on the registered (and best processed) *.mgz. Should I use the brain.mgz file for the fully processed *.mgz file? Sorry if these are naive questions, I am having a hard time understanding what is the best *.mgz file to use in conjunction with the segmented hippocampus outputs. I would like to apply a texture script to these regions of interests. Thank you, Chester ___ 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
Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer
I agree this would be best asked on the Caret list to begin with (as far as conversion from Caret formats to FreeSurfer formats), however I don’t provide Caret support either having not used it in years (I can be more helpful with Connectome Workbench stuff). Donna on the Caret list can perhaps provide further help. Peace, Matt. On 8/13/15, 12:12 PM, Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: Hi Jan have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike Harms or Matt Glasser can chime in? Bruce On Thu, 13 Aug 2015, Jan Willem Koten wrote: Dear ladies and possibly gentlemen as well, I have got a rather nasty question. I would like to import the following caret file „Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape“ into free surfer and bring it into fs average space. In a next step I would like to import the caret/fsaverage result into matlab and do some stuff with it. There seems to be a mismatch between caret and freesurfer in the vertex numbers. Has somebody every tried this? Can it be done? I am not familiar with caret and would like to avoid using it. Alternatively there is matlab toolbox for caret. But I have no clue how to get from one ico vertex system into another. Greetings Jan Jan Willem Koten (van Grevenbicht) Neurological Clinic at the RWTH Aachen Pauwelstraße 30, 52074 Aachen, Germany Telephone: (0049) (0)241 8089909 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer
Hi Matt thanks for the answer. I thought maybe someone in HCP had already imported this PALS file into FreeSurfer. cheers Bruce On Thu, 13 Aug 2015, Matt Glasser wrote: I agree this would be best asked on the Caret list to begin with (as far as conversion from Caret formats to FreeSurfer formats), however I don’t provide Caret support either having not used it in years (I can be more helpful with Connectome Workbench stuff). Donna on the Caret list can perhaps provide further help. Peace, Matt. On 8/13/15, 12:12 PM, Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: Hi Jan have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike Harms or Matt Glasser can chime in? Bruce On Thu, 13 Aug 2015, Jan Willem Koten wrote: Dear ladies and possibly gentlemen as well, I have got a rather nasty question. I would like to import the following caret file „Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape“ into free surfer and bring it into fs average space. In a next step I would like to import the caret/fsaverage result into matlab and do some stuff with it. There seems to be a mismatch between caret and freesurfer in the vertex numbers. Has somebody every tried this? Can it be done? I am not familiar with caret and would like to avoid using it. Alternatively there is matlab toolbox for caret. But I have no clue how to get from one ico vertex system into another. Greetings Jan Jan Willem Koten (van Grevenbicht) Neurological Clinic at the RWTH Aachen Pauwelstraße 30, 52074 Aachen, Germany Telephone: (0049) (0)241 8089909 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] cannot find qdec file
I'm not sure what to tell you. When I use the new file I don't get an error. When I use the old one I do. Can you run mris_preproc --debug --qdec-long long.qdec.table.dat and send me the result? On 08/13/2015 01:01 PM, Clara Kühn wrote: do you mean the one without the blank line at the end? I've attached that for you. Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 13. August 2015 18:12:40 Betreff: Re: [Freesurfer] cannot find qdec file Can you send the new qdec table file? On 08/05/2015 04:05 AM, Clara Kühn wrote: no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 4. August 2015 20:43:47 Betreff: Re: [Freesurfer] cannot find qdec file oops, sorry for the delay, thanks for the reminder. The problem is that you have a blank line at the end of your long.qdec.table.dat file. Remove the line and see if it works. doug On 08/04/2015 12:42 PM, Clara Kühn wrote: Hi Doug, did the fordoug.log file give any information about why FreeSurfer can't find my qdec file? Cheers and thanks for working on this! Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 17:16:18 Betreff: Re: [Freesurfer] cannot find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. and the actual qdec file is attached. Cheers, Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 Betreff: Re: [Freesurfer] cannot find qdec file Can you send your command line, full terminal output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 Betreff: Re: [Freesurfer] cannot find qdec file that is probably not the full path. Try typing ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat If it says it cannot find the file, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 Betreff: Re: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh It always says ERROR: cannot find qdec/long.qdec.table.dat Yes, the walkthrough asks for an input file named just qdec.table.dat, but I haven't got that. So far in the longitudinal stream there are long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat files. So I figured I'd use the long.qdec file because FS needs to get the information about the long timepoints. But it cannot find the file, even though I see it. I've also tried copying the long.qdec file and naming it qdec.table.dat but it still doesn't find it. The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and my SUBJECTS_DIR is scr/etsch2/kids/ct Can you help me see what I'm missing? Thanks a lot in advance, Clara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cannot find qdec file
Can you send the new qdec table file? On 08/05/2015 04:05 AM, Clara Kühn wrote: no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 4. August 2015 20:43:47 Betreff: Re: [Freesurfer] cannot find qdec file oops, sorry for the delay, thanks for the reminder. The problem is that you have a blank line at the end of your long.qdec.table.dat file. Remove the line and see if it works. doug On 08/04/2015 12:42 PM, Clara Kühn wrote: Hi Doug, did the fordoug.log file give any information about why FreeSurfer can't find my qdec file? Cheers and thanks for working on this! Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 17:16:18 Betreff: Re: [Freesurfer] cannot find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. and the actual qdec file is attached. Cheers, Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 Betreff: Re: [Freesurfer] cannot find qdec file Can you send your command line, full terminal output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 Betreff: Re: [Freesurfer] cannot find qdec file that is probably not the full path. Try typing ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat If it says it cannot find the file, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 Betreff: Re: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh It always says ERROR: cannot find qdec/long.qdec.table.dat Yes, the walkthrough asks for an input file named just qdec.table.dat, but I haven't got that. So far in the longitudinal stream there are long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat files. So I figured I'd use the long.qdec file because FS needs to get the information about the long timepoints. But it cannot find the file, even though I see it. I've also tried copying the long.qdec file and naming it qdec.table.dat but it still doesn't find it. The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and my SUBJECTS_DIR is scr/etsch2/kids/ct Can you help me see what I'm missing? Thanks a lot in advance, Clara ___ 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
Re: [Freesurfer] Resending my questions: Issues with first attempt in viewing Tracula output
Sorry, didn't get anything! Did you use me as the recipient (ayendiki)? On Thu, 13 Aug 2015, Leora Amira wrote: Dear Anastasia, I send (uploaded) the files on Monday. Could you please confirm that they arrived. Thank you so very much for looking into it. Leora. Leora Amira, PhD Columbia University NYS Psychiatric Institute Division of Child and Adolescent Psychiatry 1051 Riverside Drive New York, NY 10032 amir...@nyspi.columbia.edu Office: 646-774-5820 On 8/7/15, 6:17 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu wrote: Hi Leora - I regret to inform you that it's the processing that has failed, pretty much for all the tracts. I'm guessing it's an earlier preprocessing (likely registration) step that has failed. If you upload the tracula output directories (dmri, dlabel, dpath) of your subject for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Please also send your trac-all.log. Thanks! a.y On Fri, 24 Jul 2015, Leora Amira wrote: Thank you very much. From: Leora Amira amir...@nyspi.columbia.edu Date: Thursday, July 23, 2015 at 2:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Issues with first attempt in viewing Tracula output Hi, This is my first time using Tracula. I processed a large number of subjects¹ DTI scans and am now viewing the results in Freeview (I copied the commands from Tracula wiki tutorial). The images look somewhat peculiar in several ways. I am attaching screenshots with a few questions. 1. All my images look jaggedy and not smooth and beautiful like in the Tracula wiki tutorialŠ. (image 1: ilf)[IMAGE] 2. Tracts are truncated: Corpus callosum forceps are not complete (image 2)[IMAGE] 3. Tracts are displaced: Corpus callosum forceps are displaced and out of the brain template (image 3)[IMAGE] 4. All tracts seem truncated and not exactly in the right place (image 4[IMAGE] Are the errors in the viewing or, I so hope not, in the processing? And if so, what might be the errors and how to correct them? Thank you very much. Grateful. ___ 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.
