It looks like you made your txt file under windows which creates an obscure situation where there are carriage returns instead of line feeds and that causes the error. If you run 'more my_parcstats.txt' you see a bunch of ^M strings. So, you'll need to recreate it under a linux system.
doug On 03/03/2015 05:50 PM, Jin, Tony wrote: > Hi Dr. Greve (and co.), > > Good to hear that I’m using a proper command, but alas, visualizing > the surface overlay file using tksurfer confirmed that my stats didn’t > transfer. I believe I’m calling tksurfer correctly, since I replaced > the lh.parcstats file with lh.thickness, and a cortical thickness heat > map overlaid just fine. > > Would you please confirm that my parcstats.txt file is arranged > correctly? It is an ascii file with 36 lines. Here are the first few: > > ctx-lh-bankssts 0.905 > ctx-lh-caudalanteriorcingulate 0.838 > ctx-lh-caudalmiddlefrontal 0.922 > ctx-lh-cuneus 0.892 > > And here are my calls: > > > To generate overlay file: > mris_convert --annot lh.aparc.annot --parcstats parcstats.txt lh.pial > *lh.parcstats* <— new desired annotation file > > > To visualize overlay file mapped onto lh.pial surface using Tksurfer: > tksurfer <subject> lh pial -overlay *lh.parcstats* > > > To convert overlay file to ASCII for validation: > mris_convert -c *lh.parcstats* lh.pial lh.parcstats.asc > > I tried doing this with version 5.3.0 on both Mac and Linux platforms > and got the same results (zeroes across all vertices). If it helps, > I’ve attached both my —parcstats text file and the resulting overlay > file. Any ideas as to how I can successfully transfer my stats onto a > surface overlay file? > > Thank you for your assistance, > Tony > > Tony Jin > Data Technician > Dept. of Psychiatry > Stony Brook Medicine > > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Reply-To: "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Tuesday, March 3, 2015 at 11:43 AM > To: "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface > > > That is the right way (or one of them). Did you look at the result in > tksurfer? > > On 03/03/2015 11:34 AM, Jin, Tony wrote: > > Hi all, > > I’d like to map my own stats (one value per Desikan-Killiany region) > onto a subject's surface file, to create a figure similar to the > following: > > http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001&req=4 > > To do this, I tried to create a "scalar overlay file" using > mris_convert’s --parcstats option, per the following mris_convert > example: > > “”" > Create a scalar overlay file where each parcellation region > contains a single value: > mris_convert \ > --annot lh.aparc.annot \ > --parcstats lh.parcstats.txt \ > lh.white \ > lh.parcstats > > (...) > > --parcstats <infile> is the name of text file containing label/val > pairs, where label is an annot name and val is a value associated > with > that label. > “”" > > However, looking at the output file, stats didn’t seem to map to any > vertices; instead, I observed zeroes across all in both Freeview and > after conversion to ASCII (see first few lines below). I tried a few > other ways to delimit the “label/val” pairs of the "--parcstats" > file, > including using tab, space, and forward-slash, but each way seemed to > produce the same results: > > 000 -10.67346 -71.19921 6.09064 0.00000 > 001 -11.29567 -71.20504 6.32133 0.00000 > 002 -12.26970 -71.62605 6.00416 0.00000 > 003 -13.11823 -71.40913 6.45834 0.00000 > 004 -14.22002 -71.39742 6.28750 0.00000 > > So, I wonder: is using mris_convert with the --parcstats flag a > correct way to create such a map? If so, what could have gone wrong? > If not, what’s the easiest way to map my own regional stats onto a > surface? > > Your expertise is greatly appreciated; > > Thanks and all the best, > > Tony Jin > Data Technician > Dept. of Psychiatry > Stony Brook Medicine > > > This e-mail message, including any attachments, is for the sole > use of > the intended recipient(s) and may contain confidential and privileged > information. Any unauthorized review, use, disclosure or distribution > is prohibited. If you are not the intended recipient, please contact > the sender by e-mail and destroy all copies of the original. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > 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 <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
