[Freesurfer] mri_extract_label output
Hi, I would need to extract multiple labels from the aparc+aseg labelmap. I am using the mri_extract_label command, but by default all the labels of the output file are coded with the same number. Would it be possible to change such behavior, and extract multiple labels while assigning different label numbers to them? Thank you, -Michele ___ 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] TRACULA results / pathstats.overall.txt
Hi there, I have a couple questions regarding TRACULA results. When I visualize the probability distributions of all white-matter pathways simultaneously in some cases the tracts are very small, but by adjusting the threshold I am able to visualize the tract in its entire (and expected) path. So, question#1: The results included in the pathstats.overall.txt file are produced using the default threshold? It looks like the Volume is very small in those tracts that I can visualize only by playing with the threshold. I was wondering whether the DTI metrics can be also impacted. Which leads me to question#2: Do I need to re-run the whole processing (e.g. with -prior option) to get more accurate fiber tracking and DTI results, or there is a way I can adjust the threshold for computation of the DTI (and other) results? Thank you, -Michele ___ 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] Frontal WM ROI
Hi Douglas, thanks for your reply. Is there a way to rerun only WM segmentation with the threshold option, without going through the whole time-consuming FS pipeline? Thank you! On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: The unsegmented is all the WM that is further than 5mm from cortex. You can change the threshold so that it labels all of WM regardless of the distance. Other than that, I don't have much to suggest. doug On 11/18/14 6:13 PM, Michele Cavallari wrote: Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 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] Frontal WM ROI
ok, thank you very much for your prompt reply! will try to do that On Wed, Nov 19, 2014 at 11:43 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: There are two ways you can do this. 1. Make an expert options file with the contents mri_aparc2aseg --wmparc-dmax 100 Run run recon-all like recon-all -s subject -wmparc -expert YourXOptsFile 2. Look in recon-all.log for the mri_aparc2aseg command, cut and paste it into the terminal, add --wmparc-dmax 100, and run On 11/19/2014 11:34 AM, Michele Cavallari wrote: Hi Douglas, thanks for your reply. Is there a way to rerun only WM segmentation with the threshold option, without going through the whole time-consuming FS pipeline? Thank you! On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The unsegmented is all the WM that is further than 5mm from cortex. You can change the threshold so that it labels all of WM regardless of the distance. Other than that, I don't have much to suggest. doug On 11/18/14 6:13 PM, Michele Cavallari wrote: Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Frontal WM ROI
ok, so should I just re-run the recon-all with the wm option? i.e. recon-all -all --wmparc-dmax 100 On Wed, Nov 19, 2014 at 12:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michele sorry, I don't think so. You need to run to the end. The good news is that when we get V6 out you will find it is substantially faster (if you have a multi-core machine) cheers Bruce On Wed, 19 Nov 2014, Michele Cavallari wrote: Hi Douglas, thanks for your reply. Is there a way to rerun only WM segmentation with the threshold option, without going through the whole time-consuming FS pipeline?Thank you! On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: The unsegmented is all the WM that is further than 5mm from cortex. You can change the threshold so that it labels all of WM regardless of the distance. Other than that, I don't have much to suggest. doug On 11/18/14 6:13 PM, Michele Cavallari wrote: Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Frontal WM ROI
yes, I already have the FS outputs for all the subjects. Thanks On Wed, Nov 19, 2014 at 12:36 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: oh, so it's already been run all the way through? Sorry, I didn't understand that. Bruce On Wed, 19 Nov 2014, Douglas N Greve wrote: I think Michele only wants to regenerate the wmparc.mgz, so just running recon-all with --wmparc and the xopts should work On 11/19/2014 12:07 PM, Bruce Fischl wrote: Hi Michele sorry, I don't think so. You need to run to the end. The good news is that when we get V6 out you will find it is substantially faster (if you have a multi-core machine) cheers Bruce On Wed, 19 Nov 2014, Michele Cavallari wrote: Hi Douglas, thanks for your reply. Is there a way to rerun only WM segmentation with the threshold option, without going through the whole time-consuming FS pipeline?Thank you! On Tue, Nov 18, 2014 at 10:37 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: The unsegmented is all the WM that is further than 5mm from cortex. You can change the threshold so that it labels all of WM regardless of the distance. Other than that, I don't have much to suggest. doug On 11/18/14 6:13 PM, Michele Cavallari wrote: Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ 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 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.
[Freesurfer] Frontal WM ROI
Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
errata corrige: it did work! I had to re-run the whole thing including only that specific tract...and eventually it worked. On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari cavallari.mich...@gmail.com wrote: Tried...unfortunately it didn't improve On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: You can try just re-running trac-prep -prior and trac-paths for the L uncinate and no other tracts On 09/11/2014 02:58 PM, Michele Cavallari wrote: So, I re-ran the case with the set reinit option. It half worked!...in the sense that the new results show the left uncinate right, but the right-side one is still a dot (see screenshot of the brain view from the bottom). Any further suggestion? Thanks. [image: Inline image 2] On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari cavallari.mich...@gmail.com wrote: Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On 11/09/2014 17:49, Michele Cavallari wrote: Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add set reinit = 1 to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject. On Wed, 10 Sep 2014, Michele Cavallari wrote: uploaded (and activated).Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Wed, 10 Sep 2014, Michele Cavallari wrote: Hi Anastasia,I completed the tracula processing. By looking at the tractography results in the viewer I noticed that the uncinate fasciculus is pretty small (see attached screenshot). It actually appears as a small blue dot. And the problem is both on the left and right side. The other tracts look fine. I played with threshold, but the size didn't increase. So, I guess that something wrong happened with the tractography of that particular bundle. I checked the aparc+aseg output (attached): it seems right to me, but could you please double-check? Let me also know if you have any suggestions, and if you need more information or output files. Best, Michele Inline image 1 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: Hi, I was having similar errors as Michele Cavallari regarding error reading /path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Tried...unfortunately it didn't improve On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: You can try just re-running trac-prep -prior and trac-paths for the L uncinate and no other tracts On 09/11/2014 02:58 PM, Michele Cavallari wrote: So, I re-ran the case with the set reinit option. It half worked!...in the sense that the new results show the left uncinate right, but the right-side one is still a dot (see screenshot of the brain view from the bottom). Any further suggestion? Thanks. [image: Inline image 2] On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari cavallari.mich...@gmail.com wrote: Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On 11/09/2014 17:49, Michele Cavallari wrote: Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add set reinit = 1 to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject. On Wed, 10 Sep 2014, Michele Cavallari wrote: uploaded (and activated).Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Wed, 10 Sep 2014, Michele Cavallari wrote: Hi Anastasia,I completed the tracula processing. By looking at the tractography results in the viewer I noticed that the uncinate fasciculus is pretty small (see attached screenshot). It actually appears as a small blue dot. And the problem is both on the left and right side. The other tracts look fine. I played with threshold, but the size didn't increase. So, I guess that something wrong happened with the tractography of that particular bundle. I checked the aparc+aseg output (attached): it seems right to me, but could you please double-check? Let me also know if you have any suggestions, and if you need more information or output files. Best, Michele Inline image 1 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: Hi, I was having similar errors as Michele Cavallari regarding error reading /path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add set reinit = 1 to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject. On Wed, 10 Sep 2014, Michele Cavallari wrote: uploaded (and activated).Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Wed, 10 Sep 2014, Michele Cavallari wrote: Hi Anastasia,I completed the tracula processing. By looking at the tractography results in the viewer I noticed that the uncinate fasciculus is pretty small (see attached screenshot). It actually appears as a small blue dot. And the problem is both on the left and right side. The other tracts look fine. I played with threshold, but the size didn't increase. So, I guess that something wrong happened with the tractography of that particular bundle. I checked the aparc+aseg output (attached): it seems right to me, but could you please double-check? Let me also know if you have any suggestions, and if you need more information or output files. Best, Michele Inline image 1 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: Hi, I was having similar errors as Michele Cavallari regarding error reading /path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat command. I am attaching my trac-all.log and config file. Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated after I converted my dicoms to nifti using dcm2niigui (GE scanner). Can anyone tell me how dwi_frame is generated? Ludy This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On 11/09/2014 17:49, Michele Cavallari wrote: Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add set reinit = 1 to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject. On Wed, 10 Sep 2014, Michele Cavallari wrote: uploaded (and activated).Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Wed, 10 Sep 2014, Michele Cavallari wrote: Hi Anastasia,I completed the tracula processing. By looking at the tractography results in the viewer I noticed that the uncinate fasciculus is pretty small (see attached screenshot). It actually appears as a small blue dot. And the problem is both on the left and right side. The other tracts look fine. I played with threshold, but the size didn't increase. So, I guess that something wrong happened with the tractography of that particular bundle. I checked the aparc+aseg output (attached): it seems right to me, but could you please double-check? Let me also know if you have any suggestions, and if you need more information or output files. Best, Michele Inline image 1 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: Hi, I was having similar errors as Michele Cavallari regarding error reading /path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat command. I am attaching my trac-all.log and config file. Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated after I converted my dicoms to nifti using dcm2niigui (GE scanner). Can anyone tell me how dwi_frame is generated? Ludy This message is intended for the use of the person(s) to whom it may be addressed. It may contain information
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
So, I re-ran the case with the set reinit option. It half worked!...in the sense that the new results show the left uncinate right, but the right-side one is still a dot (see screenshot of the brain view from the bottom). Any further suggestion? Thanks. [image: Inline image 2] On Thu, Sep 11, 2014 at 1:36 PM, Michele Cavallari cavallari.mich...@gmail.com wrote: Thanks! it's running... On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, Don't think there is anything wrong with the attached dmrirc.tutorial file. You definitely need to add the '-c' flag infront of the path to your configuration file. Right now it reads the path to your file as a flag, which is of course not what you want. Best, Barbara On 11/09/2014 17:49, Michele Cavallari wrote: Hi Anastasia, I am probably doing something wrong with the syntax of the dmrirc file. I get this error message trac-all -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial ERROR: flag /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial unrecognized -prior /Users/michele/Desktop/tracula/sages_diff_test_tracula/sages_uncinate_dmrirc.tutorial Could you please check the attached file? On Wed, Sep 10, 2014 at 1:51 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Thanks, Michele. Hard to tell what's causing this, perhaps a bit of distortion orbitofrontally. You may be able to fix this type of thing by reinitializing the tract reconstruction: Add set reinit = 1 to your configuration file, set the pathlist to include only the left and right uncinate, and then rerun the -prior and -path steps of trac-all on this subject. On Wed, 10 Sep 2014, Michele Cavallari wrote: uploaded (and activated).Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Wed, 10 Sep 2014, Michele Cavallari wrote: Hi Anastasia,I completed the tracula processing. By looking at the tractography results in the viewer I noticed that the uncinate fasciculus is pretty small (see attached screenshot). It actually appears as a small blue dot. And the problem is both on the left and right side. The other tracts look fine. I played with threshold, but the size didn't increase. So, I guess that something wrong happened with the tractography of that particular bundle. I checked the aparc+aseg output (attached): it seems right to me, but could you please double-check? Let me also know if you have any suggestions, and if you need more information or output files. Best, Michele Inline image 1 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: Hi, I was having similar errors as Michele Cavallari regarding error reading /path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat command. I am attaching my trac-all.log and config file. Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated after I converted my dicoms to nifti using
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
uploaded (and activated). Thanks! On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michele - The anatomical segmentation does look good, but from the screenshot the DWI data seems to be noisy in the orbitofrontal area, which may be affecting the uncinate. It's hard to tell just from one slice. If you upload all the tracula output directories of this subject (dmri, dmri.bedpostX, dlabel, dpath) for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Wed, 10 Sep 2014, Michele Cavallari wrote: Hi Anastasia,I completed the tracula processing. By looking at the tractography results in the viewer I noticed that the uncinate fasciculus is pretty small (see attached screenshot). It actually appears as a small blue dot. And the problem is both on the left and right side. The other tracts look fine. I played with threshold, but the size didn't increase. So, I guess that something wrong happened with the tractography of that particular bundle. I checked the aparc+aseg output (attached): it seems right to me, but could you please double-check? Let me also know if you have any suggestions, and if you need more information or output files. Best, Michele Inline image 1 On Thu, Sep 4, 2014 at 11:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ludy - If your gradient table is formatted in 3 rows you need to either: 1. Convert it to 3 columns so you can use it with the 5.3 version of tracula, which requires the gradient table to be formatted in columns OR 2. Download the tracula update that can use gradient tables formatted in rows Hope this helps, a.y On Thu, 4 Sep 2014, ls...@bidmc.harvard.edu wrote: Hi, I was having similar errors as Michele Cavallari regarding error reading /path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs file. I did try reconfiguring my bvecs file into columns instead of row just in case, but that didn't solve the problem. It really just looks like it can't find the dwi_frame file after the mri_concat command. I am attaching my trac-all.log and config file. Running Freesurfer 5.3 on Macbook OS 10.7.5. The bvecs files were generated after I converted my dicoms to nifti using dcm2niigui (GE scanner). Can anyone tell me how dwi_frame is generated? Ludy This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Hi Barbara and Anastasia, thanks to your suggestions and help I was able to run the pre-processing step of tracula. I was using FreeSurfer 5.3, but didn't download any update. That's probably why the row configuration was not working. Anyway, I used the column configuration after manual correction for extra text due to excel formatting. Thanks again for your help. I'll get back to you as soon as the next error message pops up! Best, -Michele On Thu, Sep 4, 2014 at 5:03 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michelle - Your column-formatted gradient table (original_columns.bvec) shows up as having only 2 rows in unix (e.g. with the cat command). That's sometimes the case for text files saved from Excel or other non-unix applications. When I open your file in TextEdit on a mac and then copy-paste it into a unix text editor, it shows up fine. For row-formatted gradient tables, you have to make sure you have the latest version of tracula, as that option was added more recently: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates Hope this helps, a.y On Thu, 28 Aug 2014, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Thanks Anastasia. I figured out the right path, and I'm now running the 2nd step of tracula pipeline on that case. There was a problem with subdirectories (my fault). And also the missing 'SUBJECTS_DIR' syntax in the setenv command, as both you and Barbara pointed out. Thanks again for your help On Thu, Sep 4, 2014 at 5:22 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Michelle - Try replacing this line: setenv /Users/michele/Desktop/tracula/sages_diff_test_ tracula/SD40_1/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b with: setenv SUBJECTS_DIR /PHShome/my738/FSout (Or whatever the location of your freesurfer recons is.) a.y On Wed, 3 Sep 2014, Michele Cavallari wrote: Hi Barbara,I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P0401_e20130813_s002_ Cor7minMDEFT_T1_b/ and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/ This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz What path did you specify for the T1 segmentations (by recon-all) in your configuration file? Hope it helps, All the best, Barbara On 03.09.14 17:31, Michele Cavallari wrote: Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file. That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors). Any help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula). more original_columns.bval 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 NEURO-222:tracula_help NEURO-222$ more original_columns.bvec 0 0 0 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Hi Barbara, I checked the path. The folder with the trac-all output is is the very same folder of the dwi dicoms. Attached is the dmrirc file I am using, with all the specs. Thanks On Wed, Sep 3, 2014 at 12:59 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, You would have to make sure that the files are written to the same folder for both commands (recon-all and trac-all) Right now it seems you wrote the output of recon-all to /PHShome/my738/FSout/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b/ and trac-all output to /Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/ This is what the code was looking for but did not find: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz What path did you specify for the T1 segmentations (by recon-all) in your configuration file? Hope it helps, All the best, Barbara On 03.09.14 17:31, Michele Cavallari wrote: Hi Barbara, thanks again for your help. I checked the bvecs file using the 'more' command, and (as you pointed out) there was some extra text. This was likely due to MS-excel formatting, which I have used to reshape the bvecs file from row to column configuration. Such extra text was not part of the original bvecs file organized in rows though, but tracula was not giving errors as well. So, take home message#1 It is not true that FreeSurfer 5.3 allows both rows and columns configuration of the bvecs (as stated in the wiki page). Or at least that's not true for all the scanners. I'd recommend a column configuration of the bvecs, even with FreeSurfer 5.3. Also - take home message#2 verify that there's no extra text due to excel formatting in the reshaped bvecs file. That said, now this lead me to the next error! It seems that there's a problem with the recon-all output that I'm using (?). However, both the log file and the output of the recon-all processing seem fine to me. Here is the detail of the error message I am getting ERROR: fio_pushd: path/to/dlabel/mni And attached are the log files of both tracula pre-processing (with errors) and recon-all (apparently without errors). Any help/suggestions? Thanks. On Mon, Sep 1, 2014 at 5:51 AM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, This might be the solution - try the command 'more' in unix on your column bvec and bval, they should each have one (bval) and three (bvec) columns and no strange symbols. But you have these symbols in the bvec-file (probably because you have extra formatting information, that is not needed and an obstacle to Tracula). more original_columns.bval 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 NEURO-222:tracula_help NEURO-222$ more original_columns.bvec 0 0 0 0 0 0 ^M0 0 0 ^M0 0 0 ^M0 0 0 ^M-1 0 0 ^M-0.166 0.986 0 ^M0.11 0.664 0.74 ^M-0.901 -0.419 -0.11 ^M0.169 -0.601 0.781 ^M0.815 -0.386 0.433 ^M-0.656 0.366 0.66 ^M^M-0.582 0.8 0.143 ^M-0.9 0.259 0.35 ^M-0.693 -0.698 0.178 ^M-0.357 -0.924 -0.14 ^M-0.543 -0.488 -0.683 ^M0.525 -0.396 0.753 ^M0.639 0.689 0.341 ^M0.33 -0.013 -0.944 ^M0.524 -0.783 0.335 ^M-0.609 -0.065 -0.791 ^M-0.22 -0.233 -0.947 ^M0.004 -0.91 -0.415 ^M0.511 0.627 -0.589 ^M-0.414 0.737 0.535 ^M0.679 0.139 -0.721 ^M-0.884 -0.296 0.362 ^M-0.262 0.432 0.863 ^M-0.088 0.185 -0.979 ^M-0.294 -0.907 0.302 ^M-0.887 -0.089 -0.453 ^M-0.257 -0.443 0.859 ^M-0.086 0.867 -0.491 ^M-0.863 0.504 -0.025 You are ending up with multiple columns in the second row, please make sure they are 3 columns. Good luck, Barbara On Mon, Sep 1, 2014 at 10:36 AM, Barbara Kreilkamp bakk@googlemail.com wrote: Hi Michele, Do you use the dicoms or the nifti files as input to TRACULA? Also, I think the complete trac-all.log could be even more helpful. I am a newbie myself but I am having a similar problem, so I am trying to find a solution as well :). Best, Barbara On Fri, Aug 29, 2014 at 4:48 PM, Michele Cavallari mic...@bwh.harvard.edu wrote: Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula
Re: [Freesurfer] problems with tracula pre-processing (bvecs)
Hi Barbara, thanks for your reply. I checked the dwi series on a viewer and it looks fine: I have 1960 dicoms, corresponding to 56 slices x 35 directions specified in the bval/bvec. Also, I was able to obtain the FA and MD maps through fsl using the very same dicoms and bval/bvec. Any suggestion? Thanks On Thu, Aug 28, 2014 at 7:30 PM, Barbara Kreilkamp bakk@googlemail.com wrote: Dear Michele, I cannot find anything wrong with your bvec and bval files. Seeing as you had an errormessage related to the dwi (the one about the dwi_frame.nii.gz): Did you check that your dwi data have the same amount of volumes as entries in bvec and bval? Good luck, Barbara On 28/08/2014 22:47, Michele Cavallari wrote: Hi, I'm having some problems with the first command of the tracula pipeline. I am using FreeSurfer 5.3 on a mac (OS 10.9). The problem seems to be related to the bvecs file. I received the following error message: niiRead(): error opening file /path/to/dmri/dwi_frame.nii.gz I read some threads available on your website, but couldn't figured out a solution yet. I tried to organize the bvecs in columns, as opposed to the original configuration in rows. By doing that and re-launching the pre-processing command I obtained a differente error message: Error: bvecs and bvals don't have the same number of entries The original bvals and bvecs files seem to have the same numbers of entries to me. But the bvecs file produced by the processing - both the bvecs.norot and the bvecs files in the dmri folder - don't have all the information of the vectors. I am enclosing a zip folder with attachments: 1) original bvecs and bvals files organized in rows and columns 2) bvecs and bvals files generated by tracula 3) error logs Let me know if you need any other information. Thanks in advance for your help. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
