Hello Bruce, Sorry! The first email was too big and the mailing list rejected me. My image was already in Jpeg though.
Sincerely, Ye On Wed, Jun 26, 2013 at 5:17 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Ye, > > can you cc the list so that others can help you? 787 would usually be too > many files for an anatomical. Something on the order of 170-256 is more > typical. If you visualize them the white matter should be bright, the gray > matter darker and the CSF very dark > > > Bruce > > > On Wed, 26 Jun 2013, ye tian wrote: > > Dear Bruce, >> I just confirmed a few hours ago that I indeed have structural MRI data >> though. I have attached an example of the last 787 files from my data >> below. >> In fact, I tried to use only those to reconstruct my volumes and surfaces. >> >> Do they serve as inputs to freesurfer? >> >> Thank you very much! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 5:04 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> no, once they have been acquired you can't change anything. You >> have to hope that they also acquired structural data in addition >> to the functional data (which is quite common). You can't change >> the way your images were formed posthoc... >> >> On Wed, 26 Jun 2013, ye tian wrote: >> >> Dear Bruce, >> If I understand correctly, I should bring these >> images back to the scanner >> and change some settings. Am I right? >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:59 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> you need to know what different scan types >> were acquired. The >> ones you showed were the fMRI time-series and >> designed to >> hilight changes in blood oxygenation level, >> which is an indirect >> marker of changes in neural firing, not >> anatomy >> >> On Wed, 26 Jun 2013, ye tian wrote: >> >> Dear Bruce, >> I inherited the data from a previous >> graduate >> student. I sent out a message >> to learn more information about the >> scanner a few >> days ago. >> What information do I need to know about >> the >> scanner? >> >> Thank you so much for your time and >> effort! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:41 PM, Bruce >> Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Ye >> >> you can't convert it, you have to >> acquire it >> that way. Where did >> you get your data? >> >> Bruce >> On Wed, 26 Jun 2013, ye tian >> wrote: >> >> Dear Bruce, >> Sorry for my lack of >> knowledge. I looked >> online, but >> couldn't find how to >> convert MRI data to >> T1-weighted >> anatomical. Would >> you please shine some >> light on it? >> >> Thank you very much! >> >> Sincerely, >> Ye >> >> >> On Wed, Jun 26, 2013 at 4:21 >> PM, Bruce >> Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Ye >> >> you need to give >> recon-all a >> T1-weighted >> anatomical (e.g. >> mprage, SPGR/FLASH, >> etc...), not >> the fMRI >> data. >> >> cheers >> Bruce >> On Wed, 26 Jun 2013, >> ye tian >> wrote: >> >> Dear Bruce, >> >> Recon-all exits >> with the >> following error >> >> ERROR: input(s) >> cannot have >> multiple >> frames! >> >> >> >> $SUBJECTS_DIR/Barba50527_2/**mri/orig/001.mgz has 439 >> frames >> >> If I open >> 001.mgz using >> freeview, I >> obtain the image >> in the >> attachment saved >> as freeview >> 001.mgz.png. >> >> >> >> In order to make >> sure that >> my problem >> does not come >> from further >> upstream, I >> am including the >> major steps >> that I took >> to get to >> this error. >> >> MAJOR STEPS >> >> STEP0: >> My inherited >> data has names >> >> >> >> BARBA50527.MR.MEDITATE_**MEDITATION.#.#.year.month.day.** >> #.#.#.#.#.IMA >> where each # is >> a string of >> numbers. >> >> >> STEP1: >> The images can >> be grouped >> into five >> categories, >> according to the >> numbers in >> the names that >> occupy the >> positions of >> the red #: >> 1.1-1.3, >> 2.1, >> 3.1-3.160, >> 4.1-4.439, >> 5.1-5.439 >> >> [1] Note: Images >> from groups >> 4 & 5 are >> very >> different from >> the images of >> groups 1, 2 and >> 3. A link to >> a youtube >> video of all >> the images can >> be seen >> in note[1]. >> >> >> STEP2: >> recon-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148038.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> recon-all >> completes without >> error. >> >> [2] Note: other >> attempts >> leads to >> different errors. >> See note [2] for >> details. >> >> >> STEP3: >> recon-all -s >> Barba50527_2 >> -autorecon1 >> >> Exits with the >> error message >> at the >> beginning of the >> email. The >> number 439 >> seems to come >> from the >> number of files >> in each >> group. >> >> >> USEFUL COMMENTS >> >> >> >> >> http://www.mail-archive.com/**freesur...@nmr.mgh.harvard.** >> edu/msg23764.html<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23764.html> >> >> I will do it for >> 001.mgz and >> 002.mgz and >> will let >> you know how it >> goes. >> >> >> QUESTIONS >> 1. Do I really >> need to >> manually parse >> the sequence >> of images? If >> so, how? >> 2. I don't >> really need to >> mri_convert my >> files into >> other formats, >> e.g., >> .dcm, do I? >> 3. Each file >> from groups 4 >> and 5 have >> multiple >> images. Do I >> need to cut >> them >> into sub-images, >> each with >> one brain? >> >> Thank you very >> much! >> >> Sincerely, >> Ye >> >> >> >> >> >> NOTES: >> Note [1] >> A video of the >> data can be >> found at >> >> >> >> http://www.youtube.com/watch?**v=W8ZFGvGvHVc&list=** >> UUfGdQq3j1gqPAc4z6Spmu2g<http://www.youtube.com/watch?v=W8ZFGvGvHVc&list=UUfGdQq3j1gqPAc4z6Spmu2g> >> >> On the top left >> corner: >> the white text >> is: >> current frame >> number / total >> frame number >> the yellow text >> is: the >> name of the >> frame >> >> Note[2] >> recon-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.** >> 07.27.10.52.51 >> >> .437500.56141898.IMA >> Completes >> without error >> recon-all -s >> Barba50527_2 >> -autorecon1 >> Warning: only >> one run found >> Error: >> MRIsample(): source >> matrix has >> zero >> determinant; >> matrix is: >> EOF >> >> econ-all -s >> Barba50527_2 >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.1.1.2010.** >> 07.27.10.52.51 >> >> .437500.56141898.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.2.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.3.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.4.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148038.IMA >> -i >> >> >> >> /Path_to_data/BARBA50527.MR.**MEDITATE_MEDITATION.5.1.2010.** >> 07.27.10.52.51 >> >> .437500.56148502.IMA >> error.log: >> matrix >> dimensionality >> >> >> >> >> >> The information in this >> e-mail is >> intended only for >> the person to whom >> it is >> addressed. 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