Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences
And please let us know if you figured it out which sequence is better. Thank you, Mahmoud On Tue, Jul 11, 2017 at 4:44 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > I am not part of such a consensus. I don’t know if there have been > rigorous comparison of the two sequences or by what metrics it is being > asserted that MGH outperforms CMRR. Perhaps you could ask your source for > this recommendation why they say that? > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of "Juranek, > Jenifer" <jenifer.jura...@uth.tmc.edu> > Date: Tuesday, July 11, 2017 at 10:34 AM > To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> > Subject: [HCP-Users] CMRR vs MGH multiband/SMS sequences > > Just curious if anyone is aware of head-to-head comparisons of CMRR and > MGH MB/SMS sequences? > > Someone recently mentioned to me that “the general consensus is that MGH > outperforms CMRR”. > > Is there a “general consensus” in the research community on this issue? > Any differences between dMRI and fMRI applications? > > I’m interested in using an HCP-style acquisition protocol for a 5yr study > about to start…from what I can tell, CMRR MB sequences have been selected > across the board for HCP-style studies currently funded by NIH. > > Does anyone have any thoughts they can share? > > Many Thanks, > > Jenifer > > ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ > > Jenifer Juranek, PhD > > Associate Professor > > Department of Pediatrics > > UTHealth > > Houston, TX 77030 > > 713.500.8233 <(713)%20500-8233> > > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] files under /HCP/global/templates
Hello Matt, Today during the HCP course, I asked Michael Harms and Tim Coalson how one can create the files under /HCP/global/templates/ especially the files under 91282_Greyordinates and standard_mesh_atlases, and both of them referred me to you. Could you advise on how to create those files for a dataset other than HCP dataset? Thank you! Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] How can I attach an image?
Hello Donna, Thank you for your response. Yes, I was hoping that Matt Glasser or others who worked with Monkeys could help me. Best, Mahmoud On Friday, January 8, 2016, Donna Dierker <do...@brainvis.wustl.edu> wrote: > Hi Mahmoud, > > I see what you mean about the hcp-users archive not showing the image you > attached: > > http://www.mail-archive.com/hcp-users@humanconnectome.org/msg02225.html > > But I can assure you that when you sent the message to hcp-users, it did > come through. I'll attach it below in this reply. > > One reason why there have been no replies to the original post (with > image) is that the T1 looks like a monkey, and few people here have > experience adapting the HCP pipeline to primates. Some, probably, but not > for public release. I wish I had ideas for your original post. The head > definitely looks tilted chin down. > > Donna > > > On Jan 8, 2016, at 9:34 AM, Mahmoud <zeydab...@gmail.com > <javascript:_e(%7B%7D,'cvml','zeydab...@gmail.com');>> wrote: > > Dear Erin, > > Thank you for clarification. The reason for asking again was that I > couldn't see any image in my post, myself, when opened my message in HCP > mailing archive. So, I was wondering what could be wrong. > > I truly appreciate the time and efforts of all who try to address the > questions. > > Best, > Mahmoud > > On Fri, Jan 8, 2016 at 10:15 AM, Erin Reid <e...@brainvis.wustl.edu > <javascript:_e(%7B%7D,'cvml','e...@brainvis.wustl.edu');>> wrote: > Hi Mahmoud, > If you are referring to your tilted sagittal view message from earlier > this week, you were successful in attaching the image. It is a matter of > waiting for someone to be available to answer your question. Please be > patient with us, we will get to your question as soon as possible. > > Thank you. > > > On 1/8/16 6:28 AM, Mahmoud wrote: > > Hello All, > > How can I attach an image to the message I'm posting on HCP mailing list? > > Thank you, > Mahmoud > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > <javascript:_e(%7B%7D,'cvml','HCP-Users@humanconnectome.org');> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > <javascript:_e(%7B%7D,'cvml','HCP-Users@humanconnectome.org');> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > <javascript:_e(%7B%7D,'cvml','HCP-Users@humanconnectome.org');> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- Sent from Gmail Mobile ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] How can I attach an image?
Dear Erin, Thank you for clarification. The reason for asking again was that I couldn't see any image in my post, myself, when opened my message in HCP mailing archive. So, I was wondering what could be wrong. I truly appreciate the time and efforts of all who try to address the questions. Best, Mahmoud On Fri, Jan 8, 2016 at 10:15 AM, Erin Reid <e...@brainvis.wustl.edu> wrote: > Hi Mahmoud, > If you are referring to your tilted sagittal view message from earlier > this week, you were successful in attaching the image. It is a matter of > waiting for someone to be available to answer your question. Please be > patient > with us, we will get to your question as soon as possible. > > Thank you. > > > On 1/8/16 6:28 AM, Mahmoud wrote: > > Hello All, > > How can I attach an image to the message I'm posting on HCP mailing list? > > Thank you, > Mahmoud > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Tilted sagittal view of T1.mgz (image attached)
Hello HCP team, I apologize for re-posting. I forgot to attach the image before. Looking at results of applying HCP pipeline on my data it looks like to me that there is something wrong with intermediate images, specifically, I saw that the Sagittal plane of T1.mgz is rotated. It is noteworthy that the FreeSurferPipeline failed I believe in last recon-all step. I am attaching the screen shot of the T1.mgz here. Please let me know what you think: Thank you for your time and efforts! Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Error in FreeSurferPipeline
Dear Tim, Thank you for your efforts and kind response. Yes, the problem was with subject directory name which is resolved now and the scripts are running without error however I'm still trying to find and tweak parameters that help me to get better results. Most probably I will ask you and others more about it in near future. Best, Mahmoud On Tue, Dec 29, 2015 at 1:49 PM, Timothy B. Brown <tbbr...@wustl.edu> wrote: > Hi Mahmoud, > > Sorry for the delay in answering your question below. I was away for the > holidays for a while. > > Have you already resolved the issue you describe (the "no output filename > specified" error in the FreeSurferPipeline)? I noticed a subsequent > message from you to the hcp-users list in which you state: > > I've applied HCP pipeline scripts to our structural data and it looks like > everything goes well to the end of PostFreeSurferPipelline. > > That being the case, does that mean that you've already resolved the > problem with the "Error: no output filename specified!" in the > FreeSurferPipeline? > > If you have, you can likely ignore the remainder of this message. > > - > > I have taken a look at the log files that you sent, and it appears to me > that the FreeSurferHiresPial.sh script (which is invoked as part of the > FreeSurferPipeline) is successfully running through line 52 in the current > latest version of the FreeSurferHiresPial.sh script. That line looks like: > > 52: mri_surf2surf --s $SubjectID --sval-xyz pial.T2 --reg $regII > $mridir/orig.mgz --tval-xyz --tval pial --hemi rh > > After that line, there are statements that extract some information from > the brain.finalsurfs.mgz file and create the > //T1w//mri/c_ras.mat matrix file. > > 54: MatrixX=`mri_info $mridir/brain.finalsurfs.mgz | grep "c_r" | cut -d > "=" -f 5 | sed s/" "/""/g` > 55: MatrixY=`mri_info $mridir/brain.finalsurfs.mgz | grep "c_a" | cut -d > "=" -f 5 | sed s/" "/""/g` > 56: MatrixZ=`mri_info $mridir/brain.finalsurfs.mgz | grep "c_s" | cut -d > "=" -f 5 | sed s/" "/""/g` > 57: echo "1 0 0 ""$MatrixX" > $mridir/c_ras.mat > 58: echo "0 1 0 ""$MatrixY" >> $mridir/c_ras.mat > 59: echo "0 0 1 ""$MatrixZ" >> $mridir/c_ras.mat > 60: echo "0 0 0 1" >> $mridir/c_ras.mat > > Next is a call to mris_convert on line 62 of the FreeSurferHiresPial.sh > script. > > 62: mris_convert "$surfdir"/lh.white "$surfdir"/lh.white.surf.gii > > I don't seem to find any evidence in your log files that the call to > mris_convert is succeeding. So your run seems to be ending with the "Error: > no output filename specified!" message somewhere between lines 54 and 62. > > It seems a bit unlikely that the problem is in lines 54 through 60, but > just to check, can you confirm for me that the file > //T1w//mri/c_ras.mat exists? In the case > shown in your logs, I believe this file should actually be named: > /home/mydata/HCPReady/111_Sigma7/T1w/111_Sigma7/mir/c_ras.mat. If it > exists, is it a 4 line text file that looks something like the following? > > 1 0 0 -1. > 0 1 0 -17.5000 > 0 0 1 19. > 0 0 0 1 > > The last numeric values on each of the first three lines will probably > differ from the above. > > Assuming that the c_ras.mat file is successfully created, then I would > note that line 62 is the first use of the $surfdir variable in the > FreeSurferHiresPial.sh script (after setting its value). In the case > shown in your log files, the $surfdir variable should have a value of > /home/mydata/HCPReady/111_Signma7/T1w/111_Sigma7/surf. > > Could you please verify that such a directory exists and is writable? > > Thanks, > > Tim > > On Tue, Dec 22, 2015, at 07:06, Mahmoud wrote: > > Hello Tim and others, > > Following the previous posts, I renamed my dataset directory and ran the > PreFreeSurferPipeline on it and it looks like finished successfully. > After running the FreeSurferPipeline I got the same error "Error: no > output filename specified!" . I've attached the FreeSurferPipeline output > and error log here for you reference. > > I appreciate your help and time. > > Thank you, > Mahmoud > > On Fri, Dec 18, 2015 at 11:39 AM, Mahmoud <zeydab...@gmail.com> wrote: > > Dear Tim, > > I got it. Thank you for detailed explanation. > > Best, > Mahmoud > > On Fri, Dec 18, 2015 at 11:29 AM, Timothy B. Brown <tbbr...@wustl.edu> > wrote: > > Hi Mahmoud, > > Short answer: > > Be
[HCP-Users] Pial surface
Hello All, I've applied HCP pipeline scripts to our structural data and it looks like everything goes well to the end of PostFreeSurferPipelline. Opening the fs_LR.wb.spec file for the low-resolution mesh, it is obvious that the pial surface line (the blue line) hits the dura or is at the very outer edge of the pial surface. I was wondering which parameters and where I should tweak to get a better result. Thank you! Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Pial surface
Hello Erin, Thank you for your response. I was hoping there are some parameters to tweak so I can compare the results and see which one makes more sense. Currently, it looks to me that the occipital and temporal lobe surfaces are not accurate enough. This made the mylin maps to show less amount of myelins, colored mostly green and yellow, while I was expecting more red. Thank you, Mahmoud On Mon, Dec 28, 2015 at 1:17 PM, Erin Reid <e...@brainvis.wustl.edu> wrote: > Hi Mahmoud, > The pial (blue) surface line is intended to hit the very outer edge of > the pial surface. There are plenty of times that the image is not clear > enough for FreeSurfer to do a "perfect" job so some dura (or blood vessels) > can sometimes be included in the pial surface outline. For our purposes, > we decided not to fix these when they were minor instances (i.e. not causing > significant surface errors). > > If you are wishing to tweak the results, hopefully Mike Harms can give you > some pointers on doing so. > > Erin Reid > > On 12/28/15 10:04 AM, Mahmoud wrote: > > Hello All, > > I've applied HCP pipeline scripts to our structural data and it looks like > everything goes well to the end of PostFreeSurferPipelline. > > Opening the fs_LR.wb.spec file for the low-resolution mesh, it is obvious > that the pial surface line (the blue line) hits the dura or is at the very > outer edge of the pial surface. I was wondering which parameters and where > I should tweak to get a better result. > > Thank you! > Mahmoud > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Pial surface
>From the output log: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP On Mon, Dec 28, 2015 at 2:29 PM, Donna Dierker <do...@brainvis.wustl.edu> wrote: > What version of Freesurfer are you using? There was a specific one for > the pipelines, and the version did affect results in the medial temporal > especially, but also the insula. > > > On Dec 28, 2015, at 12:56 PM, Mahmoud <zeydab...@gmail.com> wrote: > > > Hello Erin, > > > > Thank you for your response. I was hoping there are some parameters to > tweak so I can compare the results and see which one makes more sense. > Currently, it looks to me that the occipital and temporal lobe surfaces are > not accurate enough. This made the mylin maps to show less amount of > myelins, colored mostly green and yellow, while I was expecting more red. > > > > Thank you, > > Mahmoud > > > > On Mon, Dec 28, 2015 at 1:17 PM, Erin Reid <e...@brainvis.wustl.edu> > wrote: > > Hi Mahmoud, > > The pial (blue) surface line is intended to hit the very outer edge of > the pial surface. There are plenty of times that the image is not clear > enough for FreeSurfer to do a "perfect" job so some dura (or blood vessels) > can sometimes be included in the pial surface outline. For our purposes, > we decided not to fix these when they were minor instances (i.e. not > causing significant surface errors). > > > > If you are wishing to tweak the results, hopefully Mike Harms can give > you some pointers on doing so. > > > > Erin Reid > > > > On 12/28/15 10:04 AM, Mahmoud wrote: > >> Hello All, > >> > >> I've applied HCP pipeline scripts to our structural data and it looks > like everything goes well to the end of PostFreeSurferPipelline. > >> > >> Opening the fs_LR.wb.spec file for the low-resolution mesh, it is > obvious that the pial surface line (the blue line) hits the dura or is at > the very outer edge of the pial surface. I was wondering which parameters > and where I should tweak to get a better result. > >> > >> Thank you! > >> Mahmoud > >> ___ > >> HCP-Users mailing list > >> HCP-Users@humanconnectome.org > >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > >> > > > > ___ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > > > ___ > > HCP-Users mailing list > > HCP-Users@humanconnectome.org > > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Downsampling to 1mm in FreesurferPipeline
Dear HCP developers, Could you elaborate more on this segment of Freesurferpipeline script: It is noted because of being compatible with freesurfer we have to downsample our submilimeter data to 1mm resolution. The scripts uses the following commands: flirt -interp spline -in "$T1wImage" -ref "$T1wImage" -applyisoxfm 1 -out "$T1wImageFile"_1mm.nii.gz applywarp --rel --interp=spline -i "$T1wImage" -r "$T1wImageFile"_1mm.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wImageFile"_1mm.nii.gz applywarp --rel --interp=nn -i "$T1wImageBrain" -r "$T1wImageFile"_1mm.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o "$T1wImageBrainFile"_1mm.nii.gz What is the purpose of those two "applywarp" commands? can't we use sometning like the below command to get around the 1mm resolution issue (assuming that data size is less than 255x255x255)? *mri_convert -i -o -iis 1 -ijs 1 -iks 1* Also right after the applywarp commands, this line follows: fslmaths "$T1wImageFile"_1mm.nii.gz -div $Mean -mul 150 -abs "$T1wImageFile"_1mm.nii.gz Is this for image normalization ? and from where that "150" comes ? Thank you! Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] error in loading spec file
Dear experts, Trying to open the spec file in /MNINonlinear/fsaverage_LR32K it gives me the following error in terminal: File: T2w_restore.nii.gz Path: /data/data/home/mydata/HCPReady/111_Sigma7/MNINonLinear File does not exist! File: T1w_restore.nii.gz Path: /data/data/home/mydata/HCPReady/111_Sigma7/MNINonLinear Referring to the spec file itself it's obvious that the paths to those two files are not correct: ../../../../../../../../../../data/home/mydata/HCPReady/111_Sigma7/MNINonLinear/T2w_restore.nii.gz ../../../../../../../../../../data/home/mydata/HCPReady/111_Sigma7/MNINonLinear/T1w_restore.nii.gz Any idea how it happened and how to fix it ? Thank you, Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Error in FreeSurferPipeline 12/21/2015
Dear experts, I've got a repetition of below errors in the output log of the FreesurferPipeline: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 020: -log(p) = 4.7 tol 0.00 and also a one time occurrence of this error: The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Does anyone know what they mean and how to fix them ? Thank you, Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Error in FreeSurferPipeline
Dear Tim, I got it. Thank you for detailed explanation. Best, Mahmoud On Fri, Dec 18, 2015 at 11:29 AM, Timothy B. Brown <tbbr...@wustl.edu> wrote: > Hi Mahmoud, > > Short answer: > > Because of directory structure conventions and file naming conventions > used in the pipeline scripts, you cannot rename the subject directory and > expect that the pipelines will run without (at least) also renaming a > number of other files in the subject directory. So renaming the subject > directory will break quite a number of things. > > Long answer: > > The FreeSurferPipeline in particular and the other pipeline scripts in > general depend upon a directory structure for the data that has a root > *study* folder in which each subdirectory of that *study* folder is named > for the subject id. So if the data you are processing are in a directory > named my_study, and you had only two subjects with subject ids xyz and abc, > then you would need to have xyz and abc subdirectories in your my_study > directory. > > Seems like you've got that all set up correctly initially. > > But...the pipeline scripts also depend upon file naming conventions that > use the subject id in the file names. For example, if the subject > subdirectory is named xyz, then a number of files in that directory tree > will be expected to be named starting with xyz. For example, there is an > expectation that there will be a file named my_study/xyz > /unprocessed/3T/T1_MPR1/xyz_3T_T1w_MPR1.nii.gz. Notice that the two > places the subject id is used have to match. Similarly, many of the > pipelines will generate output files that are used by subsequent pipelines > using a naming convention in which the names of the generated files will > start with the subject id. > > So, I suspect that this is the problem you are encountering. When you run > FreeSurferPipeLineBatch and tell it to process subject xyz_1, the > FreeSurferPipeline script is expecting to find a number of input files with > names that start with xyz_1. But they're not there because your xyz_1 > directory is just a copy of the original xyz directory. So many of the > files in it start with simply xyz. > > Hope that helps, > > Tim > > On Fri, Dec 18, 2015, at 07:55, Mahmoud wrote: > > Dear experts, > > After running the PreFreeSurferPipelineBatch for subjectID = xyz I changed > the ID (i.e. renamed the subject directory name) to xyz_1 and ran the > FreeSurferPipeLineBatch which ended up with this error in the error log > file (I just copied the few last lines): > > measuring cortical thickness... > writing cortical thickness estimate to 'thickness' file. > positioning took 5.6 minutes > Error: no output filename specified! > > Is this because of that name change? if so, is there any solution to it ? > > Thank you! > Mahmoud > > ___ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > -- > Timothy B. Brown > Business & Technology Application Analyst III > Pipeline Developer (Human Connectome Project) > tbbrown(at)wustl.edu > > The material in this message is private and may contain Protected > Healthcare Information (PHI). > If you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying > or the taking of any action in reliance on the contents of this > information is strictly prohibited. > If you have received this email in error, please immediately notify the > sender via telephone or > return mail. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] How to choose the parameters
Dear experts, Could someone please answer my questions below; 1- How the CorrectionSigma (sqrt 200) value was selected in PostFreeSurferPipeline.sh ? 2- How about the values for Sigma="5" , VARIABLESIGMA="4" in FreeSurferHiresPial.sh for ? I know I can easily change those values and maybe see the effect of them but wanted to do it with some prior knowledge. Thank you, Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Warnings in PostFreeSurferPipeline
Dear developers and users, I received the following warnings in the PostFreeSurferPipeline error log: ### WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 14 entries read (originally /home//hcp/local/freesurfer/average/colortable_BA.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 14 entries read (originally /home/hcp/local/freesurfer/average/colortable_BA.txt) WARNING: name collision in input name 'CTX-LH-UNKNOWN', changing one to 'CTX-LH-UNKNOWN_1' WARNING: name collision in input name 'CTX-RH-UNKNOWN', changing one to 'CTX-RH-UNKNOWN_1' WARNING: name collision in input name 'WM-LH-UNKNOWN', changing one to 'WM-LH-UNKNOWN_1' WARNING: name collision in input name 'WM-RH-UNKNOWN', changing one to 'WM-RH-UNKNOWN_1' ### The warning pattern is repeated above and below of that middle part which I just didn't copy it here. Could you please let me know what those warnings mean ? and how can I avoid them ? Thank you, Mahmoud ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
