Hi Katica
after you move the dicoms you have to run recon-all. Something like:
recon-all \
-sd /usr/local/freesurfer/subjects2 \
-s <subject id that you pick> \
-i <path to 1 file in the correct dicom series> \
-all
this will create the directory
/usr/local/freesurfer/subjects2/<subject id that you pick>
and populate it with the analysis results average 10-14 hours or so
cheers
Bruce
On Tue, 3 Sep 2013,
Boric, Katica A. wrote:
> Hi Bruce!
> So, before my subject folder was in a shared folder with the VM and my PC
(mnt/hgfs/Linux_Share/subjects)
> After the recon with errors (see first emails) I was advised to set the
subject folder (which I understand is where the dicoms are stored, but I
might be mistaken) locally to the same freesurfer home
(usr/local/freesurfer/). So I created a new folder called subjects2
(usr/local/freesurfer/subjects2) and moved a folder with dicoms of one
patien that was in the Shared folder, to this new folder. After that, I
did: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects2
> and I didn't get any "message"
> Is this specific enough? Sorry, I am really new to freesurfer!
> Thank you very much,
> Katica
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, September 03, 2013 3:05 PM
> To: Boric, Katica A.
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] error in MRI processing
>
> Hi Katicia
>
> can you be more detailed about what you did? What command did you issue
> after you moved the dicoms? Where did you move them to? In general you
> shouldn't need to move the dicoms.
> Bruce
> On Tue, 3 Sep 2013, Boric, Katica A.
> wrote:
>
>> Hi Bruce!
>> So I created a new subject folder in the same local system of freesurfer.
>> Since there already was a folder named subjects in usr/local/freesurfer I
>> named it subjects 2: /usr/local/freesufer/subjects2
>>
>> I moved the dicoms into this new folder. Then I did setenv SUBJECTS_DIR
>> /usr/local/freesurfer/subjects2
>> and nothing happened. Am I doing something wrong?
>>
>> Thanks,
>> Katica
>>
>> ________________________________________
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, September 03, 2013 12:08 PM
>> To: Boric, Katica A.
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] error in MRI processing
>>
>> oh, then
>>
>> setenv SUBJECTS_DIR new_path
>>
>>
>> On Tue, 3 Sep 2013, Boric, Katica A. wrote:
>>
>>> Thanks Bruce!
>>> So, I just move the SUBJECT_DIR folder and then setenv? I do want to set
>>> the subject directory to a new path
>>> Thanks again,
>>> Katica
>>> ________________________________________
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, September 03, 2013 12:03 PM
>>> To: Boric, Katica A.
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] error in MRI processing
>>>
>>> setenv FREESURFER_HOME /usr/local/freesurfer
>>>
>>> On Tue, 3 Sep 2013, Boric,
>>> Katica A. wrote:
>>>
>>>>
>>>>
>>>> Hi everyone!
>>>> I wrote you last Friday regarding an error at the last moment of the MRI
>>>> processing (see e-mails below)
>>>> Zeke: thanks so much for the advice, I will move the SUBJECT_DIR to the
>>>> same folder system as $FREESURFER_HOME.
>>>> Could someone please show me how to set the directory with a tcsh shell?
>>>> The path to the freesurfer home is: usr/local/freesurfer
>>>>
>>>> Thank you very much,
>>>> Katica
>>>>
>>>>
>>>> ________________________________________
>>>> From: Z K [zkauf...@nmr.mgh.harvard.edu]
>>>> Sent: Friday, August 30, 2013 12:41 PM
>>>> To: Boric, Katica A.
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] error in MRI processing
>>>>
>>>> Katica,
>>>>
>>>> The file system in the physical computer is NTFS. But it looks like the
>>>> SUBJECTS_DIR is on a mounted filesystem. And your on a virtual machine.
>>>> Unfortunately there's lots of possibilities here for some type of
>>>> incompatibility with symbolic links.
>>>>
>>>> Would it be possible for you to set the SUBJECTS_DIR to be on the same
>>>> file system as $FREESURFER_HOME (locally) in order to avoid any
>>>> potential conflicts?
>>>>
>>>> -Zeke
>>>>
>>>> On 08/30/2013 11:54 AM, Boric, Katica A. wrote:
>>>>> Hi Doug!
>>>>> I am using free surfer on a VM. The file system in the physical computer
>>>>> is NTFS.
>>>>> Thanks,
>>>>> Katica
>>>>> ________________________________________
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>>>>> [gr...@nmr.mgh.harvard.edu]
>>>>> Sent: Friday, August 30, 2013 11:46 AM
>>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>>> Subject: Re: [Freesurfer] error in MRI processing
>>>>>
>>>>> I think this error
>>>>>
>>>>> ln: failed to create symbolic link `./fsaverage': Operation not supported
>>>>>
>>>>> is a problem with your file system. Are you using a FAT file system?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 08/30/2013 11:41 AM, Boric, Katica A. wrote:
>>>>>> Hi Bruce this comes out from ls -ald $FREESURFER_HOME/subjects/fsaverage
>>>>>>
>>>>>> drwxr-xr-x. 7 root root 4096 Oct 23 2012
>>>>>> /usr/local/freesurfer/subjects/fsaverage
>>>>>> ________________________________________
>>>>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>>>>> Sent: Friday, August 30, 2013 11:15 AM
>>>>>> To: Boric, Katica A.
>>>>>> Subject: Re: [Freesurfer] error in MRI processing
>>>>>>
>>>>>> how about:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, 30 Aug 2013, Boric,
>>>>>> Katica A. wrote:
>>>>>>
>>>>>>> This comes out:
>>>>>>> drwxrwxrwx. 1 root root 0 Aug 29 11:10 /mnt/hgfs/Linux_Share/subjects
>>>>>>> ________________________________________
>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>>>>>> [fis...@nmr.mgh.harvard.edu]
>>>>>>> Sent: Friday, August 30, 2013 11:11 AM
>>>>>>> To: Boric, Katica A.
>>>>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>>>>> Subject: Re: [Freesurfer] error in MRI processing
>>>>>>>
>>>>>>> that probably means you don't have write access to the subject
>>>>>>> directory.
>>>>>>> Can you run:
>>>>>>>
>>>>>>> ls -ald /mnt/hgfs/Linux_Share/subjects
>>>>>>>
>>>>>>> On Fri, 30 Aug 2013, Boric, Katica A.
>>>>>>> wrote:
>>>>>>>
>>>>>>>> It says:
>>>>>>>> $ ln -s /usr/local/freesurfer/subjects/fsaverage
>>>>>>>> ln: failed to create symbolic link `./fsaverage': Operation not
>>>>>>>> supported
>>>>>>>>
>>>>>>>> ________________________________________
>>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>>>>>>>> [fis...@nmr.mgh.harvard.edu]
>>>>>>>> Sent: Friday, August 30, 2013 11:04 AM
>>>>>>>> To: Boric, Katica A.
>>>>>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>>>>>> Subject: Re: [Freesurfer] error in MRI processing
>>>>>>>>
>>>>>>>> can you run:
>>>>>>>>
>>>>>>>> cd /mnt/hgfs/Linux_Share/subjects
>>>>>>>> ln -s /usr/local/freesurfer/subjects/fsaverage
>>>>>>>>
>>>>>>>> and tell us what it says?
>>>>>>>> Bruce
>>>>>>>> On Fri, 30 Aug 2013, Boric,
>>>>>>>> Katica A.
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Bruce!
>>>>>>>>> Thanks for your fast response.
>>>>>>>>> /usr/local/freesurfer/subjects/fsaverage does exists!
>>>>>>>>>
>>>>>>>>> Thanks again,
>>>>>>>>> Katica
>>>>>>>>> ________________________________________
>>>>>>>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>>>>>>>> Sent: Friday, August 30, 2013 10:51 AM
>>>>>>>>> To: Boric, Katica A.
>>>>>>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> Subject: Re: [Freesurfer] error in MRI processing
>>>>>>>>>
>>>>>>>>> Hi Katica
>>>>>>>>>
>>>>>>>>> does /usr/local/freesurfer/subjects/fsaverage exist? Do you have write
>>>>>>>>> access to /mnt/hgfs/Linux_Share/subjects?
>>>>>>>>>
>>>>>>>>> cheers
>>>>>>>>> Bruce
>>>>>>>>>
>>>>>>>>> On Fri, 30 Aug 2013, Boric, Katica A. wrote:
>>>>>>>>>
>>>>>>>>>> Hi everyone!
>>>>>>>>>> I am new to freesurfer, and I was processing and MRI using "recon-all
>>>>>>>>>> -autorecon1 -autorecon2 -autorecon3" command and I have a message
>>>>>>>>>> that
>>>>>>>> the
>>>>>>>>>> processing was exited with ERRORS. When checking the recon-all. log
>>>>>>>>>> it
>>>>>>>>>> appears that these are the error (highlighted in yellow):
>>>>>>>>>>
>>>>>>>>>> #@# BA Labels lh Thu Aug 29 22:14:42 PDT 2013
>>>>>>>>>> INFO: fsaverage subject does not exist in SUBJECTS_DIR
>>>>>>>>>> INFO: Creating symlink to fsaverage subject...
>>>>>>>>>>
>>>>>>>>>> cd /mnt/hgfs/Linux_Share/subjects; ln -s
>>>>>>>>>> /usr/local/freesurfer/subjects/fsaverage; cd -
>>>>>>>>>>
>>>>>>>>>> ln: failed to create symbolic link `./fsaverage': Operation not
>>>>>>>>>> supported
>>>>>>>>>>
>>>>>>>>>> mri_label2label --srcsubject fsaverage --srclabel
>>>>>>>>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label
>>>>>>>>>> --trgsubject
>>>>>>>>>> MGH013_SurferOutput --trglabel ./lh.BA1.label --hemi lh --regmethod
>>>>>>>> surface
>>>>>>>>>> No such file or directory
>>>>>>>>>> mri_label2label: could not open label file
>>>>>>>>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label
>>>>>>>>>>
>>>>>>>>>> srclabel =
>>>>>>>>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label
>>>>>>>>>> srcsubject = fsaverage
>>>>>>>>>> trgsubject = MGH013_SurferOutput
>>>>>>>>>> trglabel = ./lh.BA1.label
>>>>>>>>>> regmethod = surface
>>>>>>>>>>
>>>>>>>>>> srchemi = lh
>>>>>>>>>> trghemi = lh
>>>>>>>>>> trgsurface = white
>>>>>>>>>> srcsurfreg = sphere.reg
>>>>>>>>>> trgsurfreg = sphere.reg
>>>>>>>>>> usehash = 1
>>>>>>>>>> Use ProjAbs = 0, 0
>>>>>>>>>> Use ProjFrac = 0, 0
>>>>>>>>>> DoPaint 0
>>>>>>>>>>
>>>>>>>>>> SUBJECTS_DIR /mnt/hgfs/Linux_Share/subjects
>>>>>>>>>> FREESURFER_HOME /usr/local/freesurfer
>>>>>>>>>> Loading source label.
>>>>>>>>>> Invalid argument
>>>>>>>>>> ERROR reading
>>>>>>>>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label
>>>>>>>>>> Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8
>>>>>>>> 20:57:42
>>>>>>>>>> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
>>>>>>>>>>
>>>>>>>>>> recon-all -s MGH013_SurferOutput exited with ERRORS at Thu Aug 29
>>>>>>>> 22:14:43
>>>>>>>>>> PDT 2013
>>>>>>>>>>
>>>>>>>>>> If any of you could give us any advice on how to fix this we would
>>>>>>>>>> really
>>>>>>>>>> appreciate it!
>>>>>>>>>> Thank you very much,
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> Katica
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Douglas N. Greve, Ph.D.
>>>>> MGH-NMR Center
>>>>> gr...@nmr.mgh.harvard.edu
>>>>> Phone Number: 617-724-2358
>>>>> Fax: 617-726-7422
>>>>>
>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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