[Freesurfer] mgz to dicom
Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ 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] defect 0
Hi All, I am running recon-all on a set of Diff images since last 2 days and it looks like FS stopped working.It says correcting defect 0 since yesterday afternoon. Any way to figure whats going on? Many Thanks Chikku #@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Applications/freesurfer/subjects/Diff1/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Diff1 lh \n reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 * Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations :10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices :0 ordering dependant retessellation: 0 use precomputed edge table :0 smooth retessellated patch :2 match retessellated patch : 1 verbose mode : 0 * INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ before topology correction, eno=-340 (nv=73648, nf=147976, ne=221964, g=171) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... 82800 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 10 into 0 -merging segment 32 into 15 -merging segment 19 into 16 -merging segment 38 into 40 36 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Diff1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8449 (-4.4225) -vertex loglikelihood: -7.8841 (-3.9420) -normal dot loglikelihood: -3.5035 (-3.5035) -quad curv loglikelihood: -6.1723 (-3.0862) Total Loglikelihood : -26.4048 CORRECTING DEFECT 0 (vertices=30266, convex hull=4754) ___ 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] Segstats
Dear FS team, Could any tell me what this numbers stands for in segstats. 3153 Right-Hippocampus 2953 2953 3254 Right-Amygdala 969 969 45 251 CC_Posterior 191 191 46 252 CC_Mid_Posterior 200 200 I am referring to this 31 53,32 54,45 251 etc is this the slice range? Many Thanks Chikku ___ 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] volume called 001.mgz
Dear All, I am getting this error message on a scan.I deleted the created subject folders and re-ran the command,but no luck.Any suggestions? Thanks in advance, CV setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni freesurfer@freesurfer-VirtualBox:~$ recon-all -i /home/freesurfer/Desktop/10035BL/T1pre/Image1 -autorecon-all -s 10035BLFS Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/10035BLFS mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 /usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz file not found or unknown file type for file /home/freesurfer/Desktop/10035BL/T1pre/Image1 # #@# MotionCor Mon Jun 10 16:03:45 CEST 2013 ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/10035BLFS/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013 For more details, see the log file /usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting freesurfer@freesurfer-VirtualBox:~$ ___ 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] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to aseg_stats.txt Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 517, in write_table(options, rows, columns, table) File "/usr/local/freesurfer/bin/asegstats2table", line 462, in write_table tw.write() File "/usr/local/freesurfer/bin/datastruct_utils.py", line 58, in write fp = open(self.filename, 'w') IOError: [Errno 13] Permission denied: 'aseg_stats.txt' freesurfer@freesurfer-VirtualBox:/usr/lib$ Many thanks Chikku ___ 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] Freesurfer-Error message
Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre... Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012 My image files, in dcm format, are at /media/sf_freesurferstudys/raw/raw_scr/T1pre : /media/sf_freesurferstudys/raw/raw_scr/T1pre> ls Image1 Image00010 Image00019 Image00028 Image00037 Image00046 Image2 Image00011 Image00020 Image00029 Image00038 Image00047 Image3 Image00012 Image00021 Image00030 Image00039 Image00048 Image4 Image00013 Image00022 Image00031 Image00040 Image00049 Image5 Image00014 Image00023 Image00032 Image00041 Image00050 Image6 Image00015 Image00024 Image00033 Image00042 Image7 Image00016 Image00025 Image00034 Image00043 Image8 Image00017 Image00026 Image00035 Image00044 Image9 Image00018 Image00027 Image00036 Image00045 Many thanks for your help. chikku ___ 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] Freesurfer-Error message
Thanks Bruce, Still no luck,this what I am getting /freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/test7 mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FreeSurfer:~/freesurfer/subjects/test1> On 4 September 2012 14:37, Bruce Fischl wrote: > if that's the name of the image file. Can you post the list on your > replies so others can answer? > > thanks > Bruce > > On Tue, 4 Sep 2012, Varghese Chikku wrote: > > Hi Bruce, >> Many thanks for you mail. >> Is this the command you referring to. >> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image1.**dcm >> -subjid test4 >> Thanks >> Chikku >> >> On 3 September 2012 17:33, Bruce Fischl >> wrote: >> Hi Chikku >> >> you need to give it the path to an image file (any one will do) and >> it will figure out the other slices that makeup >> the same series. What is the resolution of your data? 50 slices >> isn't usually enough to cover the brain at high >> enough resolution to get good thickness results. >> >> cheers >> Bruce >> >> >> On Mon, 3 Sep 2012, Varghese Chikku wrote: >> >> >> Hi, >> >> While running the following command: >> >> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre >> -subjid test2 >> >> I keep seeing the following error: >> >> ... >> >> corRead(): can't open file >> /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info >> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ >> reading from /media/sf_freesurferstudys/** >> raw/raw_scr/T1pre... >> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 >> 01:57:59 UTC >> 2009 i686 GNU/Linux >> recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 >> EDT 2012 >> >> >> My image files, in dcm format, are at >> /media/sf_freesurferstudys/**raw/raw_scr/T1pre : >> >> /media/sf_freesurferstudys/**raw/raw_scr/T1pre> ls >> Image1 Image00010 Image00019 Image00028 Image00037 >> Image00046 >> Image2 Image00011 Image00020 Image00029 Image00038 >> Image00047 >> Image3 Image00012 Image00021 Image00030 Image00039 >> Image00048 >> Image4 Image00013 Image00022 Image00031 Image00040 >> Image00049 >> Image5 Image00014 Image00023 Image00032 Image00041 >> Image00050 >> Image6 Image00015 Image00024 Image00033 Image00042 >> Image7 Image00016 Image00025 Image00034 Image00043 >> Image8 Image00017 Image00026 Image00035 Image00044 >> Image9 Image00018 Image00027 Image00036 Image00045 >> >> Many thanks for your help. >> chikku >> >> >> >> >> 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<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
[Freesurfer] process exited abnormally
Dear all, I am trying to run recon all and FS will either exists with this * child process exited abnormally*...or just a blank window appears with leaving the system to freeze.So i have to power off the VM and start all over again. Does it have to do with the system requirements.I am using VM,. Thanks a lot, chikku ___ 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] process exited abnormally
Thanks Bruce,I am currently using 4GB ram and i5 intel processor. On 8 November 2012 15:08, Bruce Fischl wrote: > how much RAM does the VM have? > > On Thu, 8 Nov 2012, Varghese Chikku wrote: > > Dear all, >> I am trying to run recon all and FS will either exists with >> this child process exited abnormally...or just a blank window >> appears with leaving the system to freeze.So i have to power off the VM >> and start all over again. >> Does it have to do with the system requirements.I am using VM,. >> Thanks a lot, >> chikku >> >> >> > > 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<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] Results Vary
Dear FS team, I processed two set of MRI data for a single patient,Thats BL scan and TP1.I ran both scans on a Mcbook Pro and a PC with Virtual machine installed. Though I was expecting the same segstats,the results vary from Macpro to VM.For eg , for BL in Mac SubCortGrayVol is 178038 but for the same images in VM the results are 177432.Does it happened to any one beforeWhats the reson its happening and how can I remedy,validate the results. Much appreciate your advice,... In Thanks Chikku. ___ 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] Delay
Dear All, I ran a test subject on VM and the process took 20 hrs to complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I have noticed this delay happening in the past as well,where VM takes 20-24 for a single patient and Mc takes 24-30 for the same.But,this time ,its was so unexpected.Why is this happening?.Which would be more accurate,and does it mean that more time FS take,the better the results? Many thanks Chikku ___ 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] Delay
Thanks Bruce,Its 64 bit. On 29 January 2013 15:12, Bruce Fischl wrote: > no, the longer time is probably because the mac version you are using is > 32 bit. > > cheers > Bruce > > > On Tue, 29 Jan 2013, Varghese Chikku wrote: > > Dear All,I ran a test subject on VM and the process took 20 hrs to >> complete.But the same images on Mc pro took 58 hours.VM is 8GB and >> Mpro >> >> is 16 GB.I have noticed this delay happening in the past as well,where >> VM takes 20-24 for a single patient and Mc takes 24-30 for the >> same.But,this time ,its was so unexpected.Why is this happening?.Which >> would be more accurate,and does it mean that more time FS take,the >> better the results? >> Many thanks >> Chikku >> >> >> > > 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<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] Delay
Thanks Nick, Please find the attached. On 29 January 2013 19:33, Nick Schmansky wrote: > Chikku, > > Can you send us your recon-all.log and recon-all.cmd files? I'd like to > investigate why it ran so slowly. > > Nick > > > On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: > > Dear All, > > I ran a test subject on VM and the process took 20 hrs to > > complete.But the same images on Mc pro took 58 hours.VM is 8GB > > and Mpro is 16 GB.I have noticed this delay happening in the past > > as well,where VM takes 20-24 for a single patient and Mc takes > > 24-30 for the same.But,this time ,its was so unexpected.Why is this > > happening?.Which would be more accurate,and does it mean that more > > time FS take,the better the results? > > Many thanks > > Chikku > > ___ > > 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. > recon-all-status.log Description: Binary data ___ 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] Delay
SubCortGrayVol on Mac is 208022 and 296990 on VM, for the same patient.Does the processing time have something to with the results,it varies a lot. On 29 January 2013 19:33, Nick Schmansky wrote: > Chikku, > > Can you send us your recon-all.log and recon-all.cmd files? I'd like to > investigate why it ran so slowly. > > Nick > > > On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote: > > Dear All, > > I ran a test subject on VM and the process took 20 hrs to > > complete.But the same images on Mc pro took 58 hours.VM is 8GB > > and Mpro is 16 GB.I have noticed this delay happening in the past > > as well,where VM takes 20-24 for a single patient and Mc takes > > 24-30 for the same.But,this time ,its was so unexpected.Why is this > > happening?.Which would be more accurate,and does it mean that more > > time FS take,the better the results? > > Many thanks > > Chikku > > ___ > > 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] cannot find eddy_correct
Dear Team, I tried to run dt_recon and the systems says *cannot find eddy_correct,Make sure FSL is installed*. So ,do I need to install the whole FSL package to run this. In Thanks Chikku ___ 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] CORRECTING DEFECT
Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processing failed for the same data set ,and patiently waited 36 hrs at Correcting Defect 10 before logging off .Do you know why this is happening.Does it have some thing to do with the data itself. In Thanks Chikku ___ 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] DEFECT 57
Hi all, One of my subject exited with error after 5 days of processing. This is what it said, CORRECTING DEFECT 57 (vertices=101022, convex hull=10822) Excessive topologic defect encountered: could not allocate 536232126 edges for retessellation Cannot allocate memory Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013 My question is this much edges normal and how much memory i need allocate to process this. Many Thanks Chikku ___ 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] libjpeg.so.62
Hi I am getting an error while using qdec. It says error while loading shared libraries ,libjpeg.so.62 cannot open shared object file No such file or directory I ran reconall with out any problem. Any idea, tx chikku ___ 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] Qdec
Dear all, I am bit confused with the Qdec process. I finished recon all for 2 time points and want to create longitudinal data.From FS tutorial I learned to create within-subject templates for processing,which is running now with recon-all -base -tp -tp ... -all. Now,in an other link of tutorial it says ,Qdec needs each subject to have a pre-computed smoothed data for the target surface ,recon-all -s -qcache So my first is question is, recon-all -base -tp -tp ... -all will do recon-all -s -qcache along or I have to run it separately. Second,recon-all -base -tp -tp ... -all is almost 12 hrs now and wondering if this is processing images from the very begining. Many Thanks chikku ___ 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] --tablefile FILE error
Dear all, I am getting and error when trying this command, asegstats2table -s truetest1 truetest2 \ --segno 11 12 17 18 \ --tablefile FILE aseg.vol.table ERROR: output table name should be specified (use --tablefile FILE) child process exited abnormally command.I tried using Any Help Chikku ___ 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] qdec.table
All, I have completed base and long runs for qdec longitudinal analysis.Now I am struggling to make qdec.table.dat.How can I do this. Tx chikku ___ 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] Error
All, Any idea how can I sort this error, Loading data table /Users/chikkuvarghese/subject/qdec/qdec.table.dat... Number of columns: 4 fsid column:1 Number of factors: 3 Number of subjects: 1 ERROR: QdecDataTable::Load: problem parsing file /Users/chikkuvarghese/subject/qdec/qdec.table.dat This line did not appear to end with a newline: truetest2.long.eFemale70 Righthippocampus 4006 Error loading the data table. Many Thanks chikku ___ 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] Permission denied
Dear FS team, I dowloaded the latest ML version of FS and tried to run a subject.But this error is coming up.Any suggestions? chikkuvarghese$ recon-all -i /Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1 mkdir: /Applications/freesurfer/subjects/BL1: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/BL1: No such file or directory. chikkus-MacBook-Pro:~ chikkuvarghese$ ___ 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] ELF class
Hi Fs Team, I am getting this errow while trying to use freeview. reesurfer@freesurfer-VirtualBox:~$ freeview freeview.bin: error while loading shared libraries: libjpeg.so.62: wrong ELF class: ELFCLASS32 Any Help Tx chikku ___ 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.
