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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K
<zkauf...@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-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K
> <zkauf...@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
>>
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