Your attachment says that none of the commands could be found. Make sure you set up your environment correctly
On 5/20/19 4:53 AM, mustafa amin wrote: > > External Email - Use Caution > > Hi Bruce, > > Thank you for your swift response as always, may I know how to convert > the more than 100 DICOM files to mgz or nifti? I noticed that the > command is for 1 file/image, please correct me if I am wrong. The > MP-RAGE file that I sent you is more than 50 images. > > I tried to follow your instruction however it did not work smoothly. > The diacom files couldn't be converted to mgz. I have attached the > command that still did not work when I used them in this email. Please > have a look and share some thoughts. Thank you for your kind attention > and cooperation. > > > Pada Jumat, 17 Mei 2019 21.14.44 WIB, Bruce Fischl > <[email protected]> menulis: > > > Hi Mustafa > > 1. Your mprage ran through recon-all fine and the results look good. The > saggital field of view is tight, so make sure that they don't crop > brain in > that direction. > > 2. Your recon-all command line is incorrect. You should point the > SUBJECTS_DIR environment variable to whereever you want to store all of > your FreeSurfer-processed data, then use the -i switch to path to the > input > volume. You can also specify SUBJECTS_DIR on the command line. So in your > case something like: > > > recon-all -i $FREESURFER_HOME/subjects/sample-001.mgz -s FS_subject001 > -sd \ > /path/to/my/subjecs -all > > should do the trick. There is also no need to convert to nifti first > > cheers > Bruce > > > On Fri, > 17 May 2019, mustafa amin wrote: > > > > > External Email - Use Caution > > > > > Hi Bruce, > > > > Herewith I attach within the email the command that didn't work when > I wanted to reconall. Please > > have a look. What about the previous dicom that I have sent to you? > Please share some thoughts.Thank > > you very much. > > > > Yours faithfully, > > > > Mustafa > > > > > > Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl > <[email protected] <mailto:[email protected]>> menulis: > > > > > > Hi Mustafa > > > > can you give us some detials? What didn't work? Can you send us the full > > command line, screen output and recon-all.log? > > > > cheers > > Bruce > > > > > > On Thu, 16 May 2019, mustafa amin wrote: > > > > > > > > External Email - Use Caution > > > > > > Hi Douglas, > > > > > > I tried to follow the instruction to recon-all the data however it > didn't work. Please give > > > some thoughts. Thank you in advance. > > > > > > Yours faithfully, > > > > > > Mustafa > > > > > > Pada Rabu, 17 April 2019 01.02.12 WIB, Greve, Douglas N.,Ph.D. > <[email protected] <mailto:[email protected]>> > > > menulis: > > > > > > > > > Hi Mustafa, why not just run recon-all on the data you have and see > > > whether it looks ok? > > > > > > On 4/15/19 7:06 AM, mustafa amin wrote: > > > > External Email - Use Caution > > > > > > > > Hi Bruce, > > > > > > > > I’ve talked to the MRI operator and she told me that the best > thing to do the MP-RAGE > > > protocol is doing the T1 weighted 3D gradient echo with SENSE, she > can’t set the TE, TR, TI > > > just like the ADNI protocol asked, though. She can set the > thickness to 1 mm. Is this set > > > up okay? > > > > > > > > I have the DIACOM files of some subjects with the set up above. > Can I send them to you to > > > look at them? > > > > > > > > I am terribly sorry for keep asking this basic question due to > we never had experience > > > doing it in Indonesia. > > > > > > > > Many thanks! > > > > > > > > > > > > Mustafa M. Amin > > > > Consultant Psychiatrist in Biological Psychiatry > > > > Department of Psychiatry > > > > Faculty of Medicine > > > > Universitas Sumatera Utara > > > > > > > >> On 2 Apr 2019, at 20.49, Bruce Fischl > <[email protected] <mailto:[email protected]>> wrote: > > > >> > > > >> Hi Mustafa > > > >> > > > >> MRI is an amazingly versatile technology that can be messed up > in an > > > >> astonishing number of ways. By far the best thing to do would > be to acquire > > > >> a dataset and run it through recon-all and see if the results look > > > >> accurate. If you have permission to do so, you are welcome to > acquire one > > > >> and send it to us to try out instead. > > > >> > > > >> cheers > > > >> Bruce > > > >> > > > >> On Tue, 2 Apr 2019, mustafa amin > > > >> wrote: > > > >> > > > >>> External Email - Use Caution > > > >>> > > > >>> Dear Freesurfer experts, > > > >>> > > > >>> I need advice, the MRI operator need to confirm whether she > had done the > > > >>> right protocol of MP-RAGE. I have attached the picture that > has been > > > >>> taken by her. Please share some thoughts. Thank you in advance. > > > >>> > > > >>> > > > >> _______________________________________________ > > > >> Freesurfer mailing list > > > >> [email protected] > <mailto:[email protected]> > > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > [email protected] > <mailto:[email protected]> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] <mailto:[email protected]> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] <mailto:[email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
