hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I should have mentioned that in the example below, you will also want to change your SUBJECTS_DIR.
$> export SUBJECTS_DIR=/Users/wieser
-Zeke
On 11/14/2014 03:13 PM, Z K wrote:
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
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
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI" (which contains all to my subjects), and use qdec and recon-all to create new files and subdirectories in the linked directory, will those new files and directories be present in the original directory "/Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI". the actual file, not just symbloic links. because dropbox is backing up the directory and dropbox does not like symbolic links
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
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.
Yes, the directories and files will all exist under the Dropbox folder and will thus be backed up by Dropbox. But I suggest you test this for yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI" (which contains all to my subjects), and use qdec and recon-all to create new files and subdirectories in the linked directory, will those new files and directories be present in the original directory "/Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI". the actual file, not just symbloic links. because dropbox is backing up the directory and dropbox does not like symbolic links
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
_______________________________________________ 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
yes, I will test it. i'm kind of new to symbolic links. thanks! Jon
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
Yes, the directories and files will all exist under the Dropbox folder and will thus be backed up by Dropbox. But I suggest you test this for yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI" (which contains all to my subjects), and use qdec and recon-all to create new files and subdirectories in the linked directory, will those new files and directories be present in the original directory "/Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI". the actual file, not just symbloic links. because dropbox is backing up the directory and dropbox does not like symbolic links
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I test ran it with the symbolic link. the symbolink link is: lrwxr-xr-x 1 wieser admin 66 Nov 14 14:17 DROPBOX_MJMRI -> /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI
I'm in the DROPBOX_MJMRI directory and have set the subjects_directory to the current directory pwd /Studies/DROPBOX_MJMRI
export SUBJECTS_DIR=$PWD I start qdec qdec opens okay. but i'm getting some errors inside:
After I load the Data table file and press "Generate Stats tables" I goto to the" design" tab and select my discrete factors
and press "Analyze"
i get the message on the command line:
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI cmdline mri_glmfit --y /Studies/DROPBOX_MJMRI/qdec/Untitled/y.mgh --fsgd /Studies/DROPBOX_MJMRI/qdec/Untitled/qdec.fsgd dods --glmdir /Studies/DROPBOX_MJMRI/qdec/Untitled --surf fsaverage lh --label /Studies/DROPBOX_MJMRI/fsaverage/label/lh.aparc.label --C /Studies/DROPBOX_MJMRI/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Studies/DROPBOX_MJMRI/qdec/Untitled/contrasts/lh-Diff-MJ-CNT-Intercept-thickness.mat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Studies/DROPBOX_MJMRI/qdec/Untitled/qdec.fsgd labelmask /Studies/DROPBOX_MJMRI/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Studies/DROPBOX_MJMRI/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Studies/DROPBOX_MJMRI/qdec/Untitled Loading y from /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Studies/DROPBOX_MJMRI/qdec/Untitled/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.83333 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Studies/DROPBOX_MJMRI/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 44 Starting fit and test Fit completed in 0.0371167 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995422, ar1std=0.001609, gstd=5.974165, fwhm=14.068083 Writing results lh-Avg-Intercept-thickness maxvox sig=1e+10 F=5529.25 at index 2 0 0 seed=1416823986 lh-Diff-MJ-CNT-Intercept-thickness maxvox sig=3.82394 F=17.2193 at index 112785 0 0 seed=1416823986 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Studies/DROPBOX_MJMRI/qdec/Untitled/contrasts.sig.mgh 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 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /Studies/DROPBOX_MJMRI/qdec/Untitled/y.fsgd INFO: ignoring tag (UWM INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed mri_read(): couldn't determine type of file /Studies/DROPBOX_MJMRI/qdec/Untitled/Dropbox ERROR: gdfRead: Couldn't read raw data at /Users/wieser/Dropbox WARNING: Could not get the graph title. WARNING: Could not get the measurement label. WARNING: Could not get the subject name. WARNING: Could not get the data file name. ERROR: Could not get number of classes. ID not found ID not found ID not found
============================================================ Completed loading of analyzed data. ID not found
the message "y /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/qdec/Untitled/y.mgh" and INFO: ignoring tag (UWM indicates that it is referencing the directory that the sym link is pointing to
after I select the analysis results that I want to look at. the command line message: ID not found
When i press "find clusters and Goto Max" and then hit "Next" to go through the clusters. the graph which show the subject values for the clust does not show up, and I get the message in the command line
Found 10 clusters Contrast: 'lh-Diff-MJ-CNT-Intercept-thickness', 10fwhm, DOF: 44 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 3.8239 112785 105.34 -8.2 -47.7 48.0 214 precuneus 2 3.2166 115393 93.03 -32.5 -87.8 -5.6 119 lateraloccipital 3 2.6664 136940 64.28 -34.3 -4.6 -39.9 111 fusiform 4 2.4832 145552 44.96 -19.2 -7.1 61.9 88 superiorfrontal 5 2.4668 108605 37.18 -63.7 -11.1 17.1 105 postcentral 6 2.4048 66572 15.49 -33.1 7.1 27.2 42 caudalmiddlefrontal 7 -2.3036 37629 19.54 -19.7 26.0 -16.4 40 lateralorbitofrontal 8 2.2686 134209 22.64 -27.9 38.8 -8.7 41 lateralorbitofrontal 9 2.0927 112660 4.52 -13.9 -13.8 43.1 15 paracentral 10 -2.0050 39586 2.40 -2.7 12.7 23.9 4 caudalanteriorcingulate ============================================================ ID not found ID not found ID not found ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation 2 3.2166 115393 93.03 -32.5 -87.8 -5.6 119 lateraloccipital ID not found ID not found ID not found ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation 3 2.6664 136940 64.28 -34.3 -4.6 -39.9 111 fusiform ID not found ID not found ID not found
can you help with this? Thanks
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
Yes, the directories and files will all exist under the Dropbox folder and will thus be backed up by Dropbox. But I suggest you test this for yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI" (which contains all to my subjects), and use qdec and recon-all to create new files and subdirectories in the linked directory, will those new files and directories be present in the original directory "/Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI". the actual file, not just symbloic links. because dropbox is backing up the directory and dropbox does not like symbolic links
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
_______________________________________________ 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
Hmmm, I was able to duplicate the issue and it looks like you might be stuck. The getcwd method resolves symbolic links to the full (real) path and in the case of using qdec, this *might* be a problem with no quick fix... other than copying the SUBJECTS_DIR onto your local machine to a path woth no spaces (obviously).
-Zeke
On 11/21/2014 12:04 PM, Jon Alan Wieser wrote:
I test ran it with the symbolic link. the symbolink link is: lrwxr-xr-x 1 wieser admin 66 Nov 14 14:17 DROPBOX_MJMRI -> /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI
I'm in the DROPBOX_MJMRI directory and have set the subjects_directory to the current directory pwd /Studies/DROPBOX_MJMRI
export SUBJECTS_DIR=$PWD I start qdec qdec opens okay. but i'm getting some errors inside:
After I load the Data table file and press "Generate Stats tables" I goto to the" design" tab and select my discrete factors
and press "Analyze"
i get the message on the command line:
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI cmdline mri_glmfit --y /Studies/DROPBOX_MJMRI/qdec/Untitled/y.mgh --fsgd /Studies/DROPBOX_MJMRI/qdec/Untitled/qdec.fsgd dods --glmdir /Studies/DROPBOX_MJMRI/qdec/Untitled --surf fsaverage lh --label /Studies/DROPBOX_MJMRI/fsaverage/label/lh.aparc.label --C /Studies/DROPBOX_MJMRI/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Studies/DROPBOX_MJMRI/qdec/Untitled/contrasts/lh-Diff-MJ-CNT-Intercept-thickness.mat sysname Darwin hostname psy-blackbird.ad.uwm.edu machine x86_64 user wieser FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Studies/DROPBOX_MJMRI/qdec/Untitled/qdec.fsgd labelmask /Studies/DROPBOX_MJMRI/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Studies/DROPBOX_MJMRI/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Studies/DROPBOX_MJMRI/qdec/Untitled Loading y from /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Studies/DROPBOX_MJMRI/qdec/Untitled/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.83333 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Studies/DROPBOX_MJMRI/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 DOF = 44 Starting fit and test Fit completed in 0.0371167 minutes Computing spatial AR1 on surface Residual: ar1mn=0.995422, ar1std=0.001609, gstd=5.974165, fwhm=14.068083 Writing results lh-Avg-Intercept-thickness maxvox sig=1e+10 F=5529.25 at index 2 0 0 seed=1416823986 lh-Diff-MJ-CNT-Intercept-thickness maxvox sig=3.82394 F=17.2193 at index 112785 0 0 seed=1416823986 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /Studies/DROPBOX_MJMRI/qdec/Untitled/contrasts.sig.mgh 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 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) gdfReadHeader: reading /Studies/DROPBOX_MJMRI/qdec/Untitled/y.fsgd INFO: ignoring tag (UWM INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed mri_read(): couldn't determine type of file /Studies/DROPBOX_MJMRI/qdec/Untitled/Dropbox ERROR: gdfRead: Couldn't read raw data at /Users/wieser/Dropbox WARNING: Could not get the graph title. WARNING: Could not get the measurement label. WARNING: Could not get the subject name. WARNING: Could not get the data file name. ERROR: Could not get number of classes. ID not found ID not found ID not found
============================================================ Completed loading of analyzed data. ID not found
the message "y /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/qdec/Untitled/y.mgh" and INFO: ignoring tag (UWM indicates that it is referencing the directory that the sym link is pointing to
after I select the analysis results that I want to look at. the command line message: ID not found
When i press "find clusters and Goto Max" and then hit "Next" to go through the clusters. the graph which show the subject values for the clust does not show up, and I get the message in the command line
Found 10 clusters Contrast: 'lh-Diff-MJ-CNT-Intercept-thickness', 10fwhm, DOF: 44 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation
1 3.8239 112785 105.34 -8.2 -47.7 48.0 214 precuneus 2 3.2166 115393 93.03 -32.5 -87.8 -5.6 119 lateraloccipital 3 2.6664 136940 64.28 -34.3 -4.6 -39.9 111 fusiform 4 2.4832 145552 44.96 -19.2 -7.1 61.9 88 superiorfrontal 5 2.4668 108605 37.18 -63.7 -11.1 17.1 105 postcentral 6 2.4048 66572 15.49 -33.1 7.1 27.2 42 caudalmiddlefrontal 7 -2.3036 37629 19.54 -19.7 26.0 -16.4 40 lateralorbitofrontal 8 2.2686 134209 22.64 -27.9 38.8 -8.7 41 lateralorbitofrontal 9 2.0927 112660 4.52 -13.9 -13.8 43.1 15 paracentral 10 -2.0050 39586 2.40 -2.7 12.7 23.9 4 caudalanteriorcingulate============================================================ ID not found ID not found ID not found ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation 2 3.2166 115393 93.03 -32.5 -87.8 -5.6 119 lateraloccipital ID not found ID not found ID not found ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation 3 2.6664 136940 64.28 -34.3 -4.6 -39.9 111 fusiform ID not found ID not found ID not found
can you help with this? Thanks
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
Yes, the directories and files will all exist under the Dropbox folder and will thus be backed up by Dropbox. But I suggest you test this for yourself and see.
-Zeke
On 11/14/2014 03:32 PM, Jon Alan Wieser wrote:
thanks Zeke,
I have created the symbolic link.
ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI DROPBOX_MJMRI
I question is , when I cd into the symbolic link directory "DROPBOX_MJMRI" (which contains all to my subjects), and use qdec and recon-all to create new files and subdirectories in the linked directory, will those new files and directories be present in the original directory "/Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI". the actual file, not just symbloic links. because dropbox is backing up the directory and dropbox does not like symbolic links
thanks!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Z K zkaufman@nmr.mgh.harvard.edu Sent: Friday, November 14, 2014 2:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] qdec and recon-all crashes
The trick in the situation is to create a symbolic link. For example:
$> cd /Users/wieser/ $> ln -s /Users/wieser/Dropbox\ (UWM\ BraIN\ Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001 MJ0001 $> recon-all -s MJ0001 -qcache
-Zeke
On 11/14/2014 02:53 PM, Jon Alan Wieser wrote:
hi freesurfer folks,
when I try to run qdec or recon-all, they crash
recon-all -s MJ0001 -qcache
if: Expression Syntax.
qdec cd: Too many arguments.
we have determined that because the subjects_directory name has spaces and ()'s in it, it is causing the two programs to crash
echo $SUBJECTS_DIR /Users/wieser/Dropbox (UWM BraIN Lab)/ImagingSuite/Blackbird/MJMRI/MJ0001
I know that linux doesn't like spaces and ()'s in the directory name, and I usually avoid them, but we have recently started using dropbox to backup our data, in Dropbox is causing the spaces and ()'s to be in the directory name. Is there any way to make recon-all and qdec run in directories that have these characters in the directory name
thanks
Jon
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Z K